SMTL ID : 4whr.1

Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-12-12-mer

Ligands

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

3N8.1: 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 3N8.3: 5 residues within 4Å: Chain B: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.167 Hydrogen bonds: B:N.159, B:R.167 3N8.4: 5 residues within 4Å: Chain C: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.167, C:I.171 Hydrogen bonds: C:R.167 3N8.6: 8 residues within 4Å: Chain D: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 Chain K: P.215 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:R.7, D:R.7 Hydrogen bonds: D:Q.41 Water bridges: D:R.7, D:Q.41, D:Q.41 3N8.7: 7 residues within 4Å: Chain D: Y.115, L.116, A.117 Chain V: L.72, R.77, M.216, D.217 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain V Hydrophobic interactions: D:Y.115, D:L.116, V:L.72 pi-Cation interactions: V:R.77 3N8.8: 8 residues within 4Å: Chain C: L.160 Chain D: S.38, I.39, P.40 Chain E: R.150, P.153 Chain K: P.215, M.216 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.40, C:L.160 3N8.9: 5 residues within 4Å: Chain D: P.32, R.33 Chain E: P.22, I.28 Ligands: TRS.14 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:P.22 Water bridges: E:R.33 Hydrogen bonds: D:R.33, D:R.33 pi-Cation interactions: D:R.33 3N8.10: 5 residues within 4Å: Chain D: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.193, D:V.201 Water bridges: D:I.195, D:A.196 3N8.12: 5 residues within 4Å: Chain E: P.32, R.33 Chain F: P.22, I.28 Ligands: TRS.14 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:P.22 Water bridges: F:R.33 Hydrogen bonds: E:R.33, E:R.33 pi-Cation interactions: E:R.33 3N8.13: 7 residues within 4Å: Chain A: L.160 Chain E: S.38, I.39, P.40 Chain F: R.150, P.153 Chain R: M.216 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.150 Hydrophobic interactions: E:P.40 3N8.15: 8 residues within 4Å: Chain E: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 Chain R: P.215 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain R Hydrophobic interactions: E:R.7, E:R.7, R:P.215 Hydrogen bonds: E:Q.41 Water bridges: E:R.7, E:Q.41, E:Q.41 Halogen bonds: E:F.8 3N8.18: 8 residues within 4Å: Chain F: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 Chain V: P.215 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:R.7, F:R.7 Hydrogen bonds: F:Q.41 Water bridges: F:R.7, F:Q.41 3N8.19: 5 residues within 4Å: Chain D: P.22, I.28 Chain F: P.32, R.33 Ligands: TRS.14 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:R.33, F:R.33 pi-Cation interactions: F:R.33 Hydrophobic interactions: D:P.22 Water bridges: D:R.33 3N8.20: 8 residues within 4Å: Chain B: L.160 Chain D: R.150, P.153 Chain F: S.38, I.39, P.40 Chain V: P.215, M.216 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: B:L.160, F:P.40 Hydrogen bonds: D:R.150 3N8.25: 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 3N8.27: 5 residues within 4Å: Chain H: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:R.167 Hydrogen bonds: H:N.159, H:R.167 3N8.28: 5 residues within 4Å: Chain I: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:R.167, I:I.171 Hydrogen bonds: I:R.167 3N8.30: 8 residues within 4Å: Chain E: P.215 Chain J: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:R.7, J:R.7 Hydrogen bonds: J:Q.41 Water bridges: J:R.7, J:Q.41, J:Q.41 3N8.31: 7 residues within 4Å: Chain J: Y.115, L.116, A.117 Chain P: L.72, R.77, M.216, D.217 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain P Hydrophobic interactions: J:Y.115, J:L.116, P:L.72 pi-Cation interactions: P:R.77 3N8.32: 8 residues within 4Å: Chain E: P.215, M.216 Chain I: L.160 Chain J: S.38, I.39, P.40 Chain K: R.150, P.153 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:L.160, J:P.40 3N8.33: 5 residues within 4Å: Chain J: P.32, R.33 Chain K: P.22, I.28 Ligands: TRS.38 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: K:P.22 Water bridges: K:R.33 Hydrogen bonds: J:R.33, J:R.33 pi-Cation interactions: J:R.33 3N8.34: 5 residues within 4Å: Chain J: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:K.193, J:V.201 Water bridges: J:I.195, J:A.196 3N8.36: 5 residues within 4Å: Chain K: P.32, R.33 Chain L: P.22, I.28 Ligands: TRS.38 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:P.22 Water bridges: L:R.33 Hydrogen bonds: K:R.33, K:R.33 pi-Cation interactions: K:R.33 3N8.37: 7 residues within 4Å: Chain G: L.160 Chain K: S.38, I.39, P.40 Chain L: R.150, P.153 Chain X: M.216 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:R.150 Hydrophobic interactions: K:P.40 3N8.39: 8 residues within 4Å: Chain K: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 Chain X: P.215 8 PLIP interactions: 7 interactions with chain K, 1 interactions with chain X Hydrophobic interactions: K:R.7, K:R.7, X:P.215 Hydrogen bonds: K:Q.41 Water bridges: K:R.7, K:Q.41, K:Q.41 Halogen bonds: K:F.8 3N8.42: 8 residues within 4Å: Chain L: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 Chain P: P.215 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:R.7, L:R.7 Hydrogen bonds: L:Q.41 Water bridges: L:R.7, L:Q.41 3N8.43: 5 residues within 4Å: Chain J: P.22, I.28 Chain L: P.32, R.33 Ligands: TRS.38 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain J Hydrogen bonds: L:R.33, L:R.33 pi-Cation interactions: L:R.33 Hydrophobic interactions: J:P.22 Water bridges: J:R.33 3N8.44: 8 residues within 4Å: Chain H: L.160 Chain J: R.150, P.153 Chain L: S.38, I.39, P.40 Chain P: P.215, M.216 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: H:L.160, L:P.40 Hydrogen bonds: J:R.150 3N8.49: 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 3N8.51: 5 residues within 4Å: Chain N: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain N Hydrophobic interactions: N:R.167 Hydrogen bonds: N:N.159, N:R.167 3N8.52: 5 residues within 4Å: Chain O: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain O Hydrophobic interactions: O:R.167, O:I.171 Hydrogen bonds: O:R.167 3N8.54: 8 residues within 4Å: Chain P: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 Chain W: P.215 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:R.7, P:R.7 Hydrogen bonds: P:Q.41 Water bridges: P:R.7, P:Q.41, P:Q.41 3N8.55: 7 residues within 4Å: Chain J: L.72, R.77, M.216, D.217 Chain P: Y.115, L.116, A.117 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain J Hydrophobic interactions: P:Y.115, P:L.116, J:L.72 pi-Cation interactions: J:R.77 3N8.56: 8 residues within 4Å: Chain O: L.160 Chain P: S.38, I.39, P.40 Chain Q: R.150, P.153 Chain W: P.215, M.216 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain O Hydrophobic interactions: P:P.40, O:L.160 3N8.57: 5 residues within 4Å: Chain P: P.32, R.33 Chain Q: P.22, I.28 Ligands: TRS.62 5 PLIP interactions: 3 interactions with chain P, 2 interactions with chain Q Hydrogen bonds: P:R.33, P:R.33 pi-Cation interactions: P:R.33 Hydrophobic interactions: Q:P.22 Water bridges: Q:R.33 3N8.58: 5 residues within 4Å: Chain P: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:K.193, P:V.201 Water bridges: P:I.195, P:A.196 3N8.60: 5 residues within 4Å: Chain Q: P.32, R.33 Chain R: P.22, I.28 Ligands: TRS.62 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 Water bridges: R:R.33 3N8.61: 7 residues within 4Å: Chain F: M.216 Chain M: L.160 Chain Q: S.38, I.39, P.40 Chain R: R.150, P.153 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain R Hydrophobic interactions: Q:P.40 Hydrogen bonds: R:R.150 3N8.63: 8 residues within 4Å: Chain F: P.215 Chain Q: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 8 PLIP interactions: 7 interactions with chain Q, 1 interactions with chain F Hydrophobic interactions: Q:R.7, Q:R.7, F:P.215 Hydrogen bonds: Q:Q.41 Water bridges: Q:R.7, Q:Q.41, Q:Q.41 Halogen bonds: Q:F.8 3N8.66: 8 residues within 4Å: Chain J: P.215 Chain R: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 5 PLIP interactions: 5 interactions with chain R Hydrophobic interactions: R:R.7, R:R.7 Hydrogen bonds: R:Q.41 Water bridges: R:R.7, R:Q.41 3N8.67: 5 residues within 4Å: Chain P: P.22, I.28 Chain R: P.32, R.33 Ligands: TRS.62 5 PLIP interactions: 2 interactions with chain P, 3 interactions with chain R Hydrophobic interactions: P:P.22 Water bridges: P:R.33 Hydrogen bonds: R:R.33, R:R.33 pi-Cation interactions: R:R.33 3N8.68: 8 residues within 4Å: Chain J: P.215, M.216 Chain N: L.160 Chain P: R.150, P.153 Chain R: S.38, I.39, P.40 3 PLIP interactions: 1 interactions with chain P, 1 interactions with chain R, 1 interactions with chain N Hydrogen bonds: P:R.150 Hydrophobic interactions: R:P.40, N:L.160 3N8.73: 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 3N8.75: 5 residues within 4Å: Chain T: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain T Hydrophobic interactions: T:R.167 Hydrogen bonds: T:N.159, T:R.167 3N8.76: 5 residues within 4Å: Chain U: N.152, P.164, R.167, E.168, I.171 3 PLIP interactions: 3 interactions with chain U Hydrophobic interactions: U:R.167, U:I.171 Hydrogen bonds: U:R.167 3N8.78: 8 residues within 4Å: Chain Q: P.215 Chain V: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 6 PLIP interactions: 6 interactions with chain V Hydrophobic interactions: V:R.7, V:R.7 Hydrogen bonds: V:Q.41 Water bridges: V:R.7, V:Q.41, V:Q.41 3N8.79: 7 residues within 4Å: Chain D: L.72, R.77, M.216, D.217 Chain V: Y.115, L.116, A.117 4 PLIP interactions: 2 interactions with chain V, 2 interactions with chain D Hydrophobic interactions: V:Y.115, V:L.116, D:L.72 pi-Cation interactions: D:R.77 3N8.80: 8 residues within 4Å: Chain Q: P.215, M.216 Chain U: L.160 Chain V: S.38, I.39, P.40 Chain W: R.150, P.153 2 PLIP interactions: 1 interactions with chain V, 1 interactions with chain U Hydrophobic interactions: V:P.40, U:L.160 3N8.81: 5 residues within 4Å: Chain V: P.32, R.33 Chain W: P.22, I.28 Ligands: TRS.86 5 PLIP interactions: 2 interactions with chain W, 3 interactions with chain V Hydrophobic interactions: W:P.22 Water bridges: W:R.33 Hydrogen bonds: V:R.33, V:R.33 pi-Cation interactions: V:R.33 3N8.82: 5 residues within 4Å: Chain V: P.187, K.193, I.195, A.196, V.201 4 PLIP interactions: 4 interactions with chain V Hydrophobic interactions: V:K.193, V:V.201 Water bridges: V:I.195, V:A.196 3N8.84: 5 residues within 4Å: Chain W: P.32, R.33 Chain X: P.22, I.28 Ligands: TRS.86 5 PLIP interactions: 3 interactions with chain W, 2 interactions with chain X Hydrogen bonds: W:R.33, W:R.33 pi-Cation interactions: W:R.33 Hydrophobic interactions: X:P.22 Water bridges: X:R.33 3N8.85: 7 residues within 4Å: Chain L: M.216 Chain S: L.160 Chain W: S.38, I.39, P.40 Chain X: R.150, P.153 2 PLIP interactions: 1 interactions with chain W, 1 interactions with chain X Hydrophobic interactions: W:P.40 Hydrogen bonds: X:R.150 3N8.87: 8 residues within 4Å: Chain L: P.215 Chain W: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 8 PLIP interactions: 7 interactions with chain W, 1 interactions with chain L Hydrophobic interactions: W:R.7, W:R.7, L:P.215 Hydrogen bonds: W:Q.41 Water bridges: W:R.7, W:Q.41, W:Q.41 Halogen bonds: W:F.8 3N8.90: 8 residues within 4Å: Chain D: P.215 Chain X: R.7, F.8, I.10, P.40, Q.41, R.231, E.236 5 PLIP interactions: 5 interactions with chain X Hydrophobic interactions: X:R.7, X:R.7 Hydrogen bonds: X:Q.41 Water bridges: X:R.7, X:Q.41 3N8.91: 5 residues within 4Å: Chain V: P.22, I.28 Chain X: P.32, R.33 Ligands: TRS.86 5 PLIP interactions: 3 interactions with chain X, 2 interactions with chain V Hydrogen bonds: X:R.33, X:R.33 pi-Cation interactions: X:R.33 Hydrophobic interactions: V:P.22 Water bridges: V:R.33 3N8.92: 8 residues within 4Å: Chain D: P.215, M.216 Chain T: L.160 Chain V: R.150, P.153 Chain X: S.38, I.39, P.40 3 PLIP interactions: 1 interactions with chain X, 1 interactions with chain T, 1 interactions with chain V Hydrophobic interactions: X:P.40, T:L.160 Hydrogen bonds: V:R.150

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

BME.2: 7 residues within 4Å: Chain A: E.69, F.92, R.94 Chain E: P.49, F.51, S.166, K.173 Ligand excluded by PLIP BME.16: 6 residues within 4Å: Chain E: Y.115, L.116, A.117 Chain K: R.77, M.216, D.217 Ligand excluded by PLIP BME.22: 3 residues within 4Å: Chain A: I.2 Chain F: M.188 Chain R: M.210 Ligand excluded by PLIP BME.23: 6 residues within 4Å: Chain F: Y.115, L.116, A.117 Chain R: R.77, M.216, D.217 Ligand excluded by PLIP BME.26: 7 residues within 4Å: Chain G: E.69, F.92, R.94 Chain K: P.49, F.51, S.166, K.173 Ligand excluded by PLIP BME.40: 6 residues within 4Å: Chain E: R.77, M.216, D.217 Chain K: Y.115, L.116, A.117 Ligand excluded by PLIP BME.46: 3 residues within 4Å: Chain G: I.2 Chain L: M.188 Chain X: M.210 Ligand excluded by PLIP BME.47: 6 residues within 4Å: Chain L: Y.115, L.116, A.117 Chain X: R.77, M.216, D.217 Ligand excluded by PLIP BME.50: 7 residues within 4Å: Chain M: E.69, F.92, R.94 Chain Q: P.49, F.51, S.166, K.173 Ligand excluded by PLIP BME.64: 6 residues within 4Å: Chain Q: Y.115, L.116, A.117 Chain W: R.77, M.216, D.217 Ligand excluded by PLIP BME.70: 3 residues within 4Å: Chain F: M.210 Chain M: I.2 Chain R: M.188 Ligand excluded by PLIP BME.71: 6 residues within 4Å: Chain F: R.77, M.216, D.217 Chain R: Y.115, L.116, A.117 Ligand excluded by PLIP BME.74: 7 residues within 4Å: Chain S: E.69, F.92, R.94 Chain W: P.49, F.51, S.166, K.173 Ligand excluded by PLIP BME.88: 6 residues within 4Å: Chain Q: R.77, M.216, D.217 Chain W: Y.115, L.116, A.117 Ligand excluded by PLIP BME.94: 3 residues within 4Å: Chain L: M.210 Chain S: I.2 Chain X: M.188 Ligand excluded by PLIP BME.95: 6 residues within 4Å: Chain L: R.77, M.216, D.217 Chain X: Y.115, L.116, A.117 Ligand excluded by PLIP

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

FE.5: 4 residues within 4Å: Chain D: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.108, D:Y.147, D:H.160, D:H.162, H2O.22 FE.11: 5 residues within 4Å: Chain E: Y.108, Y.147, H.160, H.162 Ligands: 3NJ.17 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.30 FE.24: 4 residues within 4Å: Chain F: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:Y.108, F:Y.147, F:H.160, F:H.162, H2O.36 FE.29: 4 residues within 4Å: Chain J: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:Y.108, J:Y.147, J:H.160, J:H.162, H2O.59 FE.35: 5 residues within 4Å: Chain K: Y.108, Y.147, H.160, H.162 Ligands: 3NJ.41 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.66 FE.48: 4 residues within 4Å: Chain L: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:Y.108, L:Y.147, L:H.160, L:H.162, H2O.73 FE.53: 4 residues within 4Å: Chain P: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:Y.108, P:Y.147, P:H.160, P:H.162, H2O.95 FE.59: 5 residues within 4Å: Chain Q: Y.108, Y.147, H.160, H.162 Ligands: 3NJ.65 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.102 FE.72: 4 residues within 4Å: Chain R: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:Y.108, R:Y.147, R:H.160, R:H.162, H2O.109 FE.77: 4 residues within 4Å: Chain V: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:Y.108, V:Y.147, V:H.160, V:H.162, H2O.132 FE.83: 5 residues within 4Å: Chain W: Y.108, Y.147, H.160, H.162 Ligands: 3NJ.89 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.139 FE.96: 4 residues within 4Å: Chain X: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 4 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:Y.108, X:Y.147, X:H.160, X:H.162, H2O.146

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 6 residues within 4Å: Chain D: R.33 Chain E: R.33 Chain F: R.33 Ligands: 3N8.9, 3N8.12, 3N8.19 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: D:R.33, D:R.33, F:R.33, F:R.33, E:R.33, E:R.33 TRS.38: 6 residues within 4Å: Chain J: R.33 Chain K: R.33 Chain L: R.33 Ligands: 3N8.33, 3N8.36, 3N8.43 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain K, 2 interactions with chain J Hydrogen bonds: L:R.33, L:R.33, K:R.33, K:R.33, J:R.33, J:R.33 TRS.62: 6 residues within 4Å: Chain P: R.33 Chain Q: R.33 Chain R: R.33 Ligands: 3N8.57, 3N8.60, 3N8.67 6 PLIP interactions: 2 interactions with chain P, 2 interactions with chain Q, 2 interactions with chain R Hydrogen bonds: P:R.33, P:R.33, Q:R.33, Q:R.33, R:R.33, R:R.33 TRS.86: 6 residues within 4Å: Chain V: R.33 Chain W: R.33 Chain X: R.33 Ligands: 3N8.81, 3N8.84, 3N8.91 6 PLIP interactions: 2 interactions with chain W, 2 interactions with chain V, 2 interactions with chain X Hydrogen bonds: W:R.33, W:R.33, V:R.33, V:R.33, X:R.33, X:R.33

4 x 3NJ: 4-fluorooxepine-2,7-dione(Non-covalent)

3NJ.17: 13 residues within 4Å: Chain A: T.12, G.14, P.15 Chain E: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.11 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.147, E:W.149, E:R.157, E:I.191 Hydrogen bonds: E:Q.177 Salt bridges: E:R.157, E:R.157, E:H.160, E:H.160, E:H.162, E:H.162 3NJ.41: 13 residues within 4Å: Chain G: T.12, G.14, P.15 Chain K: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.35 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:Y.147, K:W.149, K:R.157, K:I.191 Hydrogen bonds: K:Q.177 Salt bridges: K:R.157, K:R.157, K:H.160, K:H.160, K:H.162, K:H.162 3NJ.65: 13 residues within 4Å: Chain M: T.12, G.14, P.15 Chain Q: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.59 11 PLIP interactions: 11 interactions with chain Q Hydrophobic interactions: Q:Y.147, Q:W.149, Q:R.157, Q:I.191 Hydrogen bonds: Q:Q.177 Salt bridges: Q:R.157, Q:R.157, Q:H.160, Q:H.160, Q:H.162, Q:H.162 3NJ.89: 13 residues within 4Å: Chain S: T.12, G.14, P.15 Chain W: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.83 11 PLIP interactions: 11 interactions with chain W Hydrophobic interactions: W:Y.147, W:W.149, W:R.157, W:I.191 Hydrogen bonds: W:Q.177 Salt bridges: W:R.157, W:R.157, W:H.160, W:H.160, W:H.162, W:H.162

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

CL.21: 2 residues within 4Å: Chain F: R.109, P.121 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain L: R.109, P.121 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain R: R.109, P.121 Ligand excluded by PLIP CL.93: 2 residues within 4Å: Chain X: R.109, P.121 Ligand excluded by PLIP

Links

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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: ABCGHIMNOSTU
Protocatechuate 3,4-dioxygenase beta chain: DEFJKLPQRVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
C

G
A

H
E

I
C

M
A

N
E

O
C

S
A

T
E

U
C

D
D

E
B

F
F

J
D

K
B

L
F

P
D

Q
B

R
F

V
D

W
B

X
F

Protocatechuate 3,4-dioxygenase alpha chain

Protocatechuate 3,4-dioxygenase beta chain

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