SMTL ID : 4whq.1

Alkylperoxo reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-12-12-mer

Ligands

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: N.37, T.105, H.107 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: H.61, L.62, R.64 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain D: N.37, T.105, H.107 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain G: N.37, T.105, H.107 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain G: H.61, L.62, R.64 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain J: N.37, T.105, H.107 Ligand excluded by PLIP CL.77: 3 residues within 4Å: Chain M: N.37, T.105, H.107 Ligand excluded by PLIP CL.79: 3 residues within 4Å: Chain M: H.61, L.62, R.64 Ligand excluded by PLIP CL.93: 3 residues within 4Å: Chain P: N.37, T.105, H.107 Ligand excluded by PLIP CL.115: 3 residues within 4Å: Chain S: N.37, T.105, H.107 Ligand excluded by PLIP CL.117: 3 residues within 4Å: Chain S: H.61, L.62, R.64 Ligand excluded by PLIP CL.131: 3 residues within 4Å: Chain V: N.37, T.105, H.107 Ligand excluded by PLIP

68 x 3N8: 4-fluorobenzene-1,2-diol(Non-covalent)

3N8.2: 5 residues within 4Å: Chain A: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.167 Hydrogen bonds: A:R.167 3N8.4: 5 residues within 4Å: Chain B: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.167 Hydrogen bonds: B:R.167 3N8.6: 7 residues within 4Å: Chain C: P.187, K.193, I.195, A.196, P.198, V.201 Ligands: BME.10 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.193, C:K.193, C:V.201 3N8.7: 3 residues within 4Å: Chain C: R.33 Chain E: P.22, I.28 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:P.22 Water bridges: E:R.33 Hydrogen bonds: C:R.33, C:R.33 pi-Cation interactions: C:R.33 3N8.8: 8 residues within 4Å: Chain B: L.160 Chain C: S.38, I.39, P.40 Chain E: R.150, P.153 Chain W: P.215, M.216 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: B:L.160, C:P.40 Hydrogen bonds: E:R.150 3N8.12: 9 residues within 4Å: Chain B: L.23, N.28, P.29, T.30 Chain C: N.66, F.67, G.124, G.125, V.126 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.28, B:P.29, B:P.29 Hydrophobic interactions: C:V.126 pi-Stacking: C:F.67 3N8.15: 5 residues within 4Å: Chain D: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:R.167 Hydrogen bonds: D:R.167 3N8.20: 9 residues within 4Å: Chain D: L.23, N.28, P.29, T.30 Chain E: N.66, F.67, G.124, G.125, V.126 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:P.29, D:P.29 Water bridges: D:N.28 Hydrophobic interactions: E:F.67 3N8.21: 5 residues within 4Å: Chain E: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:K.193, E:K.193, E:V.201 Water bridges: E:I.195 3N8.22: 4 residues within 4Å: Chain E: R.33 Chain F: L.20, P.22, I.28 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:P.22, F:P.22 Hydrogen bonds: E:R.33, E:R.33 pi-Cation interactions: E:R.33 3N8.23: 5 residues within 4Å: Chain E: N.5, S.6, Q.230, R.231, K.232 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Q.230 Hydrogen bonds: E:Q.230 Water bridges: E:S.6, E:Q.230 3N8.28: 6 residues within 4Å: Chain C: R.150 Chain F: S.38, I.39, P.40 Chain O: P.215, M.216 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:P.40 Hydrogen bonds: F:S.38, F:S.38 3N8.29: 5 residues within 4Å: Chain C: L.20, P.22, I.28 Chain F: P.32, R.33 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:R.33, F:R.33 pi-Cation interactions: F:R.33 Hydrophobic interactions: C:L.20, C:P.22 Water bridges: C:R.33 3N8.30: 5 residues within 4Å: Chain F: P.187, K.193, I.195, A.196, V.201 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:K.193, F:K.193, F:V.201 3N8.31: 7 residues within 4Å: Chain D: L.160 Chain E: S.38, P.40 Chain F: R.150, P.153 Chain L: P.215, M.216 No protein-ligand interaction detected (PLIP) 3N8.33: 4 residues within 4Å: Chain A: L.5 Chain F: R.83, V.85, D.224 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain F Hydrophobic interactions: A:L.5, F:V.85, F:V.85, F:D.224 Hydrogen bonds: F:R.83 Water bridges: F:R.83, F:Y.136 3N8.36: 8 residues within 4Å: Chain A: A.26, G.27, N.28 Chain F: Y.108, R.109, H.110, K.111, L.119 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:R.109 Halogen bonds: F:Y.108 3N8.40: 5 residues within 4Å: Chain G: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:R.167 Hydrogen bonds: G:R.167 3N8.42: 5 residues within 4Å: Chain H: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:R.167 Hydrogen bonds: H:R.167 3N8.44: 7 residues within 4Å: Chain I: P.187, K.193, I.195, A.196, P.198, V.201 Ligands: BME.48 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:K.193, I:K.193, I:V.201 3N8.45: 3 residues within 4Å: Chain I: R.33 Chain K: P.22, I.28 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain I Hydrophobic interactions: K:P.22 Water bridges: K:R.33 Hydrogen bonds: I:R.33, I:R.33 pi-Cation interactions: I:R.33 3N8.46: 8 residues within 4Å: Chain H: L.160 Chain I: S.38, I.39, P.40 Chain K: R.150, P.153 Chain Q: P.215, M.216 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: H:L.160, I:P.40 Hydrogen bonds: K:R.150 3N8.50: 9 residues within 4Å: Chain H: L.23, N.28, P.29, T.30 Chain I: N.66, F.67, G.124, G.125, V.126 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:N.28, H:P.29, H:P.29 Hydrophobic interactions: I:V.126 pi-Stacking: I:F.67 3N8.53: 5 residues within 4Å: Chain J: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:R.167 Hydrogen bonds: J:R.167 3N8.58: 9 residues within 4Å: Chain J: L.23, N.28, P.29, T.30 Chain K: N.66, F.67, G.124, G.125, V.126 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:P.29, J:P.29 Water bridges: J:N.28 Hydrophobic interactions: K:F.67 3N8.59: 5 residues within 4Å: Chain K: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:K.193, K:K.193, K:V.201 Water bridges: K:I.195 3N8.60: 4 residues within 4Å: Chain K: R.33 Chain L: L.20, P.22, I.28 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:P.22, L:P.22 Hydrogen bonds: K:R.33, K:R.33 pi-Cation interactions: K:R.33 3N8.61: 5 residues within 4Å: Chain K: N.5, S.6, Q.230, R.231, K.232 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:Q.230 Hydrogen bonds: K:Q.230 Water bridges: K:S.6, K:Q.230 3N8.66: 6 residues within 4Å: Chain I: R.150 Chain L: S.38, I.39, P.40 Chain U: P.215, M.216 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:P.40 Hydrogen bonds: L:S.38, L:S.38 3N8.67: 5 residues within 4Å: Chain I: L.20, P.22, I.28 Chain L: P.32, R.33 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain L Hydrophobic interactions: I:L.20, I:P.22 Water bridges: I:R.33 Hydrogen bonds: L:R.33, L:R.33 pi-Cation interactions: L:R.33 3N8.68: 5 residues within 4Å: Chain L: P.187, K.193, I.195, A.196, V.201 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:K.193, L:K.193, L:V.201 3N8.69: 7 residues within 4Å: Chain F: P.215, M.216 Chain J: L.160 Chain K: S.38, P.40 Chain L: R.150, P.153 No protein-ligand interaction detected (PLIP) 3N8.71: 4 residues within 4Å: Chain G: L.5 Chain L: R.83, V.85, D.224 7 PLIP interactions: 6 interactions with chain L, 1 interactions with chain G Hydrophobic interactions: L:V.85, L:V.85, L:D.224, G:L.5 Hydrogen bonds: L:R.83 Water bridges: L:R.83, L:Y.136 3N8.74: 8 residues within 4Å: Chain G: A.26, G.27, N.28 Chain L: Y.108, R.109, H.110, K.111, L.119 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:R.109 Halogen bonds: L:Y.108 3N8.78: 5 residues within 4Å: Chain M: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:R.167 Hydrogen bonds: M:R.167 3N8.80: 5 residues within 4Å: Chain N: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:R.167 Hydrogen bonds: N:R.167 3N8.82: 7 residues within 4Å: Chain O: P.187, K.193, I.195, A.196, P.198, V.201 Ligands: BME.86 3 PLIP interactions: 3 interactions with chain O Hydrophobic interactions: O:K.193, O:K.193, O:V.201 3N8.83: 3 residues within 4Å: Chain O: R.33 Chain Q: P.22, I.28 5 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain O Hydrophobic interactions: Q:P.22 Water bridges: Q:R.33 Hydrogen bonds: O:R.33, O:R.33 pi-Cation interactions: O:R.33 3N8.84: 8 residues within 4Å: Chain K: P.215, M.216 Chain N: L.160 Chain O: S.38, I.39, P.40 Chain Q: R.150, P.153 3 PLIP interactions: 1 interactions with chain N, 1 interactions with chain O, 1 interactions with chain Q Hydrophobic interactions: N:L.160, O:P.40 Hydrogen bonds: Q:R.150 3N8.88: 9 residues within 4Å: Chain N: L.23, N.28, P.29, T.30 Chain O: N.66, F.67, G.124, G.125, V.126 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain O Hydrogen bonds: N:N.28, N:P.29, N:P.29 Hydrophobic interactions: O:V.126 pi-Stacking: O:F.67 3N8.91: 5 residues within 4Å: Chain P: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:R.167 Hydrogen bonds: P:R.167 3N8.96: 9 residues within 4Å: Chain P: L.23, N.28, P.29, T.30 Chain Q: N.66, F.67, G.124, G.125, V.126 4 PLIP interactions: 1 interactions with chain Q, 3 interactions with chain P Hydrophobic interactions: Q:F.67 Hydrogen bonds: P:P.29, P:P.29 Water bridges: P:N.28 3N8.97: 5 residues within 4Å: Chain Q: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain Q Hydrophobic interactions: Q:K.193, Q:K.193, Q:V.201 Water bridges: Q:I.195 3N8.98: 4 residues within 4Å: Chain Q: R.33 Chain R: L.20, P.22, I.28 5 PLIP interactions: 3 interactions with chain Q, 2 interactions with chain R Hydrogen bonds: Q:R.33, Q:R.33 pi-Cation interactions: Q:R.33 Hydrophobic interactions: R:P.22, R:P.22 3N8.99: 5 residues within 4Å: Chain Q: N.5, S.6, Q.230, R.231, K.232 4 PLIP interactions: 4 interactions with chain Q Hydrophobic interactions: Q:Q.230 Hydrogen bonds: Q:Q.230 Water bridges: Q:S.6, Q:Q.230 3N8.104: 6 residues within 4Å: Chain C: P.215, M.216 Chain O: R.150 Chain R: S.38, I.39, P.40 3 PLIP interactions: 3 interactions with chain R Hydrophobic interactions: R:P.40 Hydrogen bonds: R:S.38, R:S.38 3N8.105: 5 residues within 4Å: Chain O: L.20, P.22, I.28 Chain R: P.32, R.33 6 PLIP interactions: 3 interactions with chain O, 3 interactions with chain R Hydrophobic interactions: O:L.20, O:P.22 Water bridges: O:R.33 Hydrogen bonds: R:R.33, R:R.33 pi-Cation interactions: R:R.33 3N8.106: 5 residues within 4Å: Chain R: P.187, K.193, I.195, A.196, V.201 3 PLIP interactions: 3 interactions with chain R Hydrophobic interactions: R:K.193, R:K.193, R:V.201 3N8.107: 7 residues within 4Å: Chain P: L.160 Chain Q: S.38, P.40 Chain R: R.150, P.153 Chain X: P.215, M.216 No protein-ligand interaction detected (PLIP) 3N8.109: 4 residues within 4Å: Chain M: L.5 Chain R: R.83, V.85, D.224 8 PLIP interactions: 7 interactions with chain R, 1 interactions with chain M Hydrophobic interactions: R:V.85, R:V.85, R:D.224, M:L.5 Hydrogen bonds: R:R.83 Water bridges: R:R.83, R:Y.136, R:Y.136 3N8.112: 8 residues within 4Å: Chain M: A.26, G.27, N.28 Chain R: Y.108, R.109, H.110, K.111, L.119 2 PLIP interactions: 2 interactions with chain R Hydrophobic interactions: R:R.109 Halogen bonds: R:Y.108 3N8.116: 5 residues within 4Å: Chain S: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain S Hydrophobic interactions: S:R.167 Hydrogen bonds: S:R.167 3N8.118: 5 residues within 4Å: Chain T: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain T Hydrophobic interactions: T:R.167 Hydrogen bonds: T:R.167 3N8.120: 7 residues within 4Å: Chain U: P.187, K.193, I.195, A.196, P.198, V.201 Ligands: BME.124 3 PLIP interactions: 3 interactions with chain U Hydrophobic interactions: U:K.193, U:K.193, U:V.201 3N8.121: 3 residues within 4Å: Chain U: R.33 Chain W: P.22, I.28 5 PLIP interactions: 3 interactions with chain U, 2 interactions with chain W Hydrogen bonds: U:R.33, U:R.33 pi-Cation interactions: U:R.33 Hydrophobic interactions: W:P.22 Water bridges: W:R.33 3N8.122: 8 residues within 4Å: Chain E: P.215, M.216 Chain T: L.160 Chain U: S.38, I.39, P.40 Chain W: R.150, P.153 3 PLIP interactions: 1 interactions with chain T, 1 interactions with chain U, 1 interactions with chain W Hydrophobic interactions: T:L.160, U:P.40 Hydrogen bonds: W:R.150 3N8.126: 9 residues within 4Å: Chain T: L.23, N.28, P.29, T.30 Chain U: N.66, F.67, G.124, G.125, V.126 5 PLIP interactions: 2 interactions with chain U, 3 interactions with chain T Hydrophobic interactions: U:V.126 pi-Stacking: U:F.67 Hydrogen bonds: T:N.28, T:P.29, T:P.29 3N8.129: 5 residues within 4Å: Chain V: N.152, P.164, R.167, E.168, I.171 2 PLIP interactions: 2 interactions with chain V Hydrophobic interactions: V:R.167 Hydrogen bonds: V:R.167 3N8.134: 9 residues within 4Å: Chain V: L.23, N.28, P.29, T.30 Chain W: N.66, F.67, G.124, G.125, V.126 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain W Hydrogen bonds: V:P.29, V:P.29 Water bridges: V:N.28 Hydrophobic interactions: W:F.67 3N8.135: 5 residues within 4Å: Chain W: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain W Hydrophobic interactions: W:K.193, W:K.193, W:V.201 Water bridges: W:I.195 3N8.136: 4 residues within 4Å: Chain W: R.33 Chain X: L.20, P.22, I.28 5 PLIP interactions: 2 interactions with chain X, 3 interactions with chain W Hydrophobic interactions: X:P.22, X:P.22 Hydrogen bonds: W:R.33, W:R.33 pi-Cation interactions: W:R.33 3N8.137: 5 residues within 4Å: Chain W: N.5, S.6, Q.230, R.231, K.232 4 PLIP interactions: 4 interactions with chain W Hydrophobic interactions: W:Q.230 Hydrogen bonds: W:Q.230 Water bridges: W:S.6, W:Q.230 3N8.142: 6 residues within 4Å: Chain I: P.215, M.216 Chain U: R.150 Chain X: S.38, I.39, P.40 3 PLIP interactions: 3 interactions with chain X Hydrophobic interactions: X:P.40 Hydrogen bonds: X:S.38, X:S.38 3N8.143: 5 residues within 4Å: Chain U: L.20, P.22, I.28 Chain X: P.32, R.33 6 PLIP interactions: 3 interactions with chain U, 3 interactions with chain X Hydrophobic interactions: U:L.20, U:P.22 Water bridges: U:R.33 Hydrogen bonds: X:R.33, X:R.33 pi-Cation interactions: X:R.33 3N8.144: 5 residues within 4Å: Chain X: P.187, K.193, I.195, A.196, V.201 3 PLIP interactions: 3 interactions with chain X Hydrophobic interactions: X:K.193, X:K.193, X:V.201 3N8.145: 7 residues within 4Å: Chain R: P.215, M.216 Chain V: L.160 Chain W: S.38, P.40 Chain X: R.150, P.153 No protein-ligand interaction detected (PLIP) 3N8.147: 4 residues within 4Å: Chain S: L.5 Chain X: R.83, V.85, D.224 8 PLIP interactions: 7 interactions with chain X, 1 interactions with chain S Hydrophobic interactions: X:V.85, X:V.85, X:D.224, S:L.5 Hydrogen bonds: X:R.83 Water bridges: X:R.83, X:Y.136, X:Y.136 3N8.150: 8 residues within 4Å: Chain S: A.26, G.27, N.28 Chain X: Y.108, R.109, H.110, K.111, L.119 2 PLIP interactions: 2 interactions with chain X Hydrophobic interactions: X:R.109 Halogen bonds: X:Y.108

12 x FE: FE (III) ION(Non-covalent)

FE.5: 3 residues within 4Å: Chain C: Y.108, H.160, H.162 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.108, C:H.160, C:H.162, H2O.15 FE.19: 4 residues within 4Å: Chain E: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:Y.108, E:Y.147, E:H.160, E:H.162, H2O.28 FE.27: 5 residues within 4Å: Chain F: Y.108, Y.147, H.160, H.162 Ligands: 3N9.38 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:Y.108, F:Y.147, F:H.160, F:H.162 FE.43: 3 residues within 4Å: Chain I: Y.108, H.160, H.162 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:Y.108, I:H.160, I:H.162, H2O.50 FE.57: 4 residues within 4Å: Chain K: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:Y.108, K:Y.147, K:H.160, K:H.162, H2O.62 FE.65: 5 residues within 4Å: Chain L: Y.108, Y.147, H.160, H.162 Ligands: 3N9.76 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:Y.108, L:Y.147, L:H.160, L:H.162 FE.81: 3 residues within 4Å: Chain O: Y.108, H.160, H.162 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:Y.108, O:H.160, O:H.162, H2O.84 FE.95: 4 residues within 4Å: Chain Q: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:Y.108, Q:Y.147, Q:H.160, Q:H.162, H2O.96 FE.103: 5 residues within 4Å: Chain R: Y.108, Y.147, H.160, H.162 Ligands: 3N9.114 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:Y.108, R:Y.147, R:H.160, R:H.162 FE.119: 3 residues within 4Å: Chain U: Y.108, H.160, H.162 4 PLIP interactions: 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:Y.108, U:H.160, U:H.162, H2O.118 FE.133: 4 residues within 4Å: Chain W: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:Y.108, W:Y.147, W:H.160, W:H.162, H2O.131 FE.141: 5 residues within 4Å: Chain X: Y.108, Y.147, H.160, H.162 Ligands: 3N9.152 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:Y.108, X:Y.147, X:H.160, X:H.162

32 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.9: 3 residues within 4Å: Chain C: T.21, P.22, D.23 Ligand excluded by PLIP BME.10: 4 residues within 4Å: Chain C: I.186, Q.202, I.205 Ligands: 3N8.6 Ligand excluded by PLIP BME.14: 5 residues within 4Å: Chain C: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.16: 6 residues within 4Å: Chain D: E.168, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP BME.24: 5 residues within 4Å: Chain E: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.32: 4 residues within 4Å: Chain F: S.6, Q.230, R.231, K.232 Ligand excluded by PLIP BME.34: 4 residues within 4Å: Chain F: Q.203, R.222, F.223, D.224 Ligand excluded by PLIP BME.35: 5 residues within 4Å: Chain F: G.182, D.183, I.186, P.187, I.205 Ligand excluded by PLIP BME.47: 3 residues within 4Å: Chain I: T.21, P.22, D.23 Ligand excluded by PLIP BME.48: 4 residues within 4Å: Chain I: I.186, Q.202, I.205 Ligands: 3N8.44 Ligand excluded by PLIP BME.52: 5 residues within 4Å: Chain I: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.54: 6 residues within 4Å: Chain J: E.168, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP BME.62: 5 residues within 4Å: Chain K: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.70: 4 residues within 4Å: Chain L: S.6, Q.230, R.231, K.232 Ligand excluded by PLIP BME.72: 4 residues within 4Å: Chain L: Q.203, R.222, F.223, D.224 Ligand excluded by PLIP BME.73: 5 residues within 4Å: Chain L: G.182, D.183, I.186, P.187, I.205 Ligand excluded by PLIP BME.85: 3 residues within 4Å: Chain O: T.21, P.22, D.23 Ligand excluded by PLIP BME.86: 4 residues within 4Å: Chain O: I.186, Q.202, I.205 Ligands: 3N8.82 Ligand excluded by PLIP BME.90: 5 residues within 4Å: Chain O: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.92: 6 residues within 4Å: Chain P: E.168, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP BME.100: 5 residues within 4Å: Chain Q: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.108: 4 residues within 4Å: Chain R: S.6, Q.230, R.231, K.232 Ligand excluded by PLIP BME.110: 4 residues within 4Å: Chain R: Q.203, R.222, F.223, D.224 Ligand excluded by PLIP BME.111: 5 residues within 4Å: Chain R: G.182, D.183, I.186, P.187, I.205 Ligand excluded by PLIP BME.123: 3 residues within 4Å: Chain U: T.21, P.22, D.23 Ligand excluded by PLIP BME.124: 4 residues within 4Å: Chain U: I.186, Q.202, I.205 Ligands: 3N8.120 Ligand excluded by PLIP BME.128: 5 residues within 4Å: Chain U: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.130: 6 residues within 4Å: Chain V: E.168, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP BME.138: 5 residues within 4Å: Chain W: Q.203, I.205, R.222, F.223, D.224 Ligand excluded by PLIP BME.146: 4 residues within 4Å: Chain X: S.6, Q.230, R.231, K.232 Ligand excluded by PLIP BME.148: 4 residues within 4Å: Chain X: Q.203, R.222, F.223, D.224 Ligand excluded by PLIP BME.149: 5 residues within 4Å: Chain X: G.182, D.183, I.186, P.187, I.205 Ligand excluded by PLIP

12 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.11: 3 residues within 4Å: Chain C: R.109, D.120, P.121 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.120 BCT.13: 6 residues within 4Å: Chain B: N.28 Chain C: Y.108, R.109, H.110, K.111, L.119 No protein-ligand interaction detected (PLIP) BCT.37: 2 residues within 4Å: Chain F: R.83 Chain K: K.90 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain F Hydrogen bonds: K:K.90, F:R.83, F:R.83 Water bridges: F:D.134 BCT.49: 3 residues within 4Å: Chain I: R.109, D.120, P.121 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.120 BCT.51: 6 residues within 4Å: Chain H: N.28 Chain I: Y.108, R.109, H.110, K.111, L.119 No protein-ligand interaction detected (PLIP) BCT.75: 2 residues within 4Å: Chain E: K.90 Chain L: R.83 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain E Hydrogen bonds: L:R.83, L:R.83, E:K.90 Water bridges: L:D.134 BCT.87: 3 residues within 4Å: Chain O: R.109, D.120, P.121 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:D.120 BCT.89: 6 residues within 4Å: Chain N: N.28 Chain O: Y.108, R.109, H.110, K.111, L.119 No protein-ligand interaction detected (PLIP) BCT.113: 2 residues within 4Å: Chain R: R.83 Chain W: K.90 3 PLIP interactions: 1 interactions with chain W, 2 interactions with chain R Hydrogen bonds: W:K.90, R:R.83, R:R.83 BCT.125: 3 residues within 4Å: Chain U: R.109, D.120, P.121 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:D.120 BCT.127: 6 residues within 4Å: Chain T: N.28 Chain U: Y.108, R.109, H.110, K.111, L.119 No protein-ligand interaction detected (PLIP) BCT.151: 2 residues within 4Å: Chain Q: K.90 Chain X: R.83 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain Q Hydrogen bonds: X:R.83, X:R.83, Q:K.90

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.18: 5 residues within 4Å: Chain B: Q.163, Q.165 Chain D: H.61, L.62, R.64 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:L.62, B:Q.163, B:Q.165 Water bridges: D:R.64, D:R.64 Salt bridges: D:H.61, D:R.64 SO4.56: 5 residues within 4Å: Chain H: Q.163, Q.165 Chain J: H.61, L.62, R.64 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain H Hydrogen bonds: J:L.62, H:Q.163, H:Q.165 Water bridges: J:R.64, J:R.64 Salt bridges: J:H.61, J:R.64 SO4.94: 5 residues within 4Å: Chain N: Q.163, Q.165 Chain P: H.61, L.62, R.64 7 PLIP interactions: 5 interactions with chain P, 2 interactions with chain N Hydrogen bonds: P:L.62, N:Q.163, N:Q.165 Water bridges: P:R.64, P:R.64 Salt bridges: P:H.61, P:R.64 SO4.132: 5 residues within 4Å: Chain T: Q.163, Q.165 Chain V: H.61, L.62, R.64 7 PLIP interactions: 5 interactions with chain V, 2 interactions with chain T Hydrogen bonds: V:L.62, T:Q.163, T:Q.165 Water bridges: V:R.64, V:R.64 Salt bridges: V:H.61, V:R.64

4 x NA: SODIUM ION(Non-functional Binders)

NA.25: 3 residues within 4Å: Chain E: T.21, P.22, D.23 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.21, E:D.23 NA.63: 3 residues within 4Å: Chain K: T.21, P.22, D.23 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:T.21, K:D.23 NA.101: 3 residues within 4Å: Chain Q: T.21, P.22, D.23 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:T.21, Q:D.23 NA.139: 3 residues within 4Å: Chain W: T.21, P.22, D.23 2 PLIP interactions: 2 interactions with chain W Hydrogen bonds: W:T.21, W:D.23

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 9 residues within 4Å: Chain E: R.7, F.8, I.10, Q.41, R.231, E.236 Chain L: A.213, N.214, P.215 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain L Hydrogen bonds: E:F.8, E:Q.41, E:R.231, E:E.236, E:E.236 Water bridges: E:R.7, E:I.10, E:Q.41, E:Q.41, L:N.214 GOL.64: 9 residues within 4Å: Chain F: A.213, N.214, P.215 Chain K: R.7, F.8, I.10, Q.41, R.231, E.236 10 PLIP interactions: 9 interactions with chain K, 1 interactions with chain F Hydrogen bonds: K:F.8, K:Q.41, K:R.231, K:E.236, K:E.236 Water bridges: K:R.7, K:I.10, K:Q.41, K:Q.41, F:N.214 GOL.102: 9 residues within 4Å: Chain Q: R.7, F.8, I.10, Q.41, R.231, E.236 Chain X: A.213, N.214, P.215 9 PLIP interactions: 8 interactions with chain Q, 1 interactions with chain X Hydrogen bonds: Q:F.8, Q:Q.41, Q:R.231, Q:E.236 Water bridges: Q:R.7, Q:I.10, Q:Q.41, Q:Q.41, X:N.214 GOL.140: 9 residues within 4Å: Chain R: A.213, N.214, P.215 Chain W: R.7, F.8, I.10, Q.41, R.231, E.236 9 PLIP interactions: 8 interactions with chain W, 1 interactions with chain R Hydrogen bonds: W:F.8, W:Q.41, W:R.231, W:E.236 Water bridges: W:R.7, W:I.10, W:Q.41, W:Q.41, R:N.214

4 x 3N9: (6S)-4-fluoro-6-hydroperoxy-6-hydroxycyclohexa-2,4-dien-1-one(Non-covalent)

3N9.38: 13 residues within 4Å: Chain A: T.12, G.14, P.15, Y.16 Chain F: Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.27 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:Y.147, F:W.149, F:I.191 Hydrogen bonds: F:R.157, F:Q.177 Water bridges: A:Y.16, A:Y.16 3N9.76: 13 residues within 4Å: Chain G: T.12, G.14, P.15, Y.16 Chain L: Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.65 7 PLIP interactions: 5 interactions with chain L, 2 interactions with chain G Hydrophobic interactions: L:Y.147, L:W.149, L:I.191 Hydrogen bonds: L:R.157, L:Q.177 Water bridges: G:Y.16, G:Y.16 3N9.114: 13 residues within 4Å: Chain M: T.12, G.14, P.15, Y.16 Chain R: Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.103 7 PLIP interactions: 5 interactions with chain R, 2 interactions with chain M Hydrophobic interactions: R:Y.147, R:W.149, R:I.191 Hydrogen bonds: R:R.157, R:Q.177 Water bridges: M:Y.16, M:Y.16 3N9.152: 13 residues within 4Å: Chain S: T.12, G.14, P.15, Y.16 Chain X: Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.141 7 PLIP interactions: 2 interactions with chain S, 5 interactions with chain X Water bridges: S:Y.16, S:Y.16 Hydrophobic interactions: X:Y.147, X:W.149, X:I.191 Hydrogen bonds: X:R.157, X:Q.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knoot, C.J. et al., Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2014-12-31

Peptides

Protocatechuate 3,4-dioxygenase alpha chain: ABDGHJMNPSTV
Protocatechuate 3,4-dioxygenase beta chain: CEFIKLOQRUWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

D
C

G
A

H
E

J
C

M
A

N
E

P
C

S
A

T
E

V
C

C
F

E
D

F
B

I
F

K
D

L
B

O
F

Q
D

R
B

U
F

W
D

X
B

Protocatechuate 3,4-dioxygenase alpha chain

Protocatechuate 3,4-dioxygenase beta chain

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