SMTL ID : 3lxv.1

Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-12-12-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.37, A:T.105 Water bridges: A:R.38 Salt bridges: A:R.38, A:H.107 SO4.16: 4 residues within 4Å: Chain C: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.37, C:T.105 Water bridges: C:R.38 Salt bridges: C:R.38, C:H.107 SO4.29: 3 residues within 4Å: Chain E: N.37, T.105, H.107 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.37, E:N.37, E:T.105 Salt bridges: E:H.107 SO4.44: 4 residues within 4Å: Chain G: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:N.37, G:T.105 Water bridges: G:R.38 Salt bridges: G:R.38, G:H.107 SO4.59: 4 residues within 4Å: Chain I: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:N.37, I:T.105 Water bridges: I:R.38 Salt bridges: I:R.38, I:H.107 SO4.72: 3 residues within 4Å: Chain K: N.37, T.105, H.107 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:N.37, K:N.37, K:T.105 Salt bridges: K:H.107 SO4.87: 4 residues within 4Å: Chain M: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain M Hydrogen bonds: M:N.37, M:T.105 Water bridges: M:R.38 Salt bridges: M:R.38, M:H.107 SO4.102: 4 residues within 4Å: Chain O: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain O Hydrogen bonds: O:N.37, O:T.105 Water bridges: O:R.38 Salt bridges: O:R.38, O:H.107 SO4.115: 3 residues within 4Å: Chain Q: N.37, T.105, H.107 4 PLIP interactions: 4 interactions with chain Q Hydrogen bonds: Q:N.37, Q:N.37, Q:T.105 Salt bridges: Q:H.107 SO4.130: 4 residues within 4Å: Chain S: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain S Hydrogen bonds: S:N.37, S:T.105 Water bridges: S:R.38 Salt bridges: S:R.38, S:H.107 SO4.145: 4 residues within 4Å: Chain U: N.37, R.38, T.105, H.107 5 PLIP interactions: 5 interactions with chain U Hydrogen bonds: U:N.37, U:T.105 Water bridges: U:R.38 Salt bridges: U:R.38, U:H.107 SO4.158: 3 residues within 4Å: Chain W: N.37, T.105, H.107 4 PLIP interactions: 4 interactions with chain W Hydrogen bonds: W:N.37, W:N.37, W:T.105 Salt bridges: W:H.107

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: R.38, L.39, A.40, K.41, Y.83, N.84, L.85, N.87, A.88, F.89, N.90 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain B: Q.203, I.205, K.207, R.222, F.223, D.224 Chain I: I.2 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain B: R.7, F.8, I.10, Q.41, R.231 Chain R: M.210, N.211, A.213, P.215 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain D: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain B: P.22, I.28 Chain D: R.33 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain D: I.186, V.201, Q.202, I.205 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain E: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.45: 11 residues within 4Å: Chain G: R.38, L.39, A.40, K.41, Y.83, N.84, L.85, N.87, A.88, F.89, N.90 Ligand excluded by PLIP GOL.51: 7 residues within 4Å: Chain C: I.2 Chain H: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.52: 9 residues within 4Å: Chain H: R.7, F.8, I.10, Q.41, R.231 Chain X: M.210, N.211, A.213, P.215 Ligand excluded by PLIP GOL.63: 6 residues within 4Å: Chain J: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.64: 3 residues within 4Å: Chain H: P.22, I.28 Chain J: R.33 Ligand excluded by PLIP GOL.65: 4 residues within 4Å: Chain J: I.186, V.201, Q.202, I.205 Ligand excluded by PLIP GOL.73: 6 residues within 4Å: Chain K: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.88: 11 residues within 4Å: Chain M: R.38, L.39, A.40, K.41, Y.83, N.84, L.85, N.87, A.88, F.89, N.90 Ligand excluded by PLIP GOL.94: 7 residues within 4Å: Chain N: Q.203, I.205, K.207, R.222, F.223, D.224 Chain U: I.2 Ligand excluded by PLIP GOL.95: 9 residues within 4Å: Chain F: M.210, N.211, A.213, P.215 Chain N: R.7, F.8, I.10, Q.41, R.231 Ligand excluded by PLIP GOL.106: 6 residues within 4Å: Chain P: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.107: 3 residues within 4Å: Chain N: P.22, I.28 Chain P: R.33 Ligand excluded by PLIP GOL.108: 4 residues within 4Å: Chain P: I.186, V.201, Q.202, I.205 Ligand excluded by PLIP GOL.116: 6 residues within 4Å: Chain Q: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.131: 11 residues within 4Å: Chain S: R.38, L.39, A.40, K.41, Y.83, N.84, L.85, N.87, A.88, F.89, N.90 Ligand excluded by PLIP GOL.137: 7 residues within 4Å: Chain O: I.2 Chain T: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.138: 9 residues within 4Å: Chain L: M.210, N.211, A.213, P.215 Chain T: R.7, F.8, I.10, Q.41, R.231 Ligand excluded by PLIP GOL.149: 6 residues within 4Å: Chain V: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.150: 3 residues within 4Å: Chain T: P.22, I.28 Chain V: R.33 Ligand excluded by PLIP GOL.151: 4 residues within 4Å: Chain V: I.186, V.201, Q.202, I.205 Ligand excluded by PLIP GOL.159: 6 residues within 4Å: Chain W: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP

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

BME.3: 3 residues within 4Å: Chain A: P.42, H.48, K.180 Ligand excluded by PLIP BME.4: 6 residues within 4Å: Chain A: L.23, N.28, P.29 Chain B: N.66, F.67, V.126 Ligand excluded by PLIP BME.10: 3 residues within 4Å: Chain B: F.56, C.129, L.130 Ligand excluded by PLIP BME.11: 2 residues within 4Å: Chain B: D.132, S.133 Ligand excluded by PLIP BME.12: 6 residues within 4Å: Chain B: R.150, P.153 Chain D: S.38, I.39, P.40 Chain H: P.215 Ligand excluded by PLIP BME.17: 4 residues within 4Å: Chain C: N.152, A.153, P.164, R.167 Ligand excluded by PLIP BME.23: 3 residues within 4Å: Chain D: H.234, F.235 Chain H: H.61 Ligand excluded by PLIP BME.25: 5 residues within 4Å: Chain D: R.7, F.8, R.231 Chain H: A.213, P.215 Ligand excluded by PLIP BME.31: 6 residues within 4Å: Chain E: N.152, A.153, L.158, N.159, R.167, E.168 Ligand excluded by PLIP BME.32: 6 residues within 4Å: Chain E: P.15, Y.16, R.133 Chain F: W.149, R.150 Ligands: 4NC.43 Ligand excluded by PLIP BME.34: 4 residues within 4Å: Chain F: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.35: 3 residues within 4Å: Chain F: H.234, F.235 Chain V: S.138 Ligand excluded by PLIP BME.36: 3 residues within 4Å: Chain F: R.107, P.118, L.119 Ligand excluded by PLIP BME.37: 1 residues within 4Å: Chain F: R.83 Ligand excluded by PLIP BME.38: 3 residues within 4Å: Chain D: P.22, I.28 Chain F: R.33 Ligand excluded by PLIP BME.46: 3 residues within 4Å: Chain G: P.42, H.48, K.180 Ligand excluded by PLIP BME.47: 6 residues within 4Å: Chain G: L.23, N.28, P.29 Chain H: N.66, F.67, V.126 Ligand excluded by PLIP BME.53: 3 residues within 4Å: Chain H: F.56, C.129, L.130 Ligand excluded by PLIP BME.54: 2 residues within 4Å: Chain H: D.132, S.133 Ligand excluded by PLIP BME.55: 6 residues within 4Å: Chain B: P.215 Chain H: R.150, P.153 Chain J: S.38, I.39, P.40 Ligand excluded by PLIP BME.60: 4 residues within 4Å: Chain I: N.152, A.153, P.164, R.167 Ligand excluded by PLIP BME.66: 3 residues within 4Å: Chain B: H.61 Chain J: H.234, F.235 Ligand excluded by PLIP BME.68: 5 residues within 4Å: Chain B: A.213, P.215 Chain J: R.7, F.8, R.231 Ligand excluded by PLIP BME.74: 6 residues within 4Å: Chain K: N.152, A.153, L.158, N.159, R.167, E.168 Ligand excluded by PLIP BME.75: 6 residues within 4Å: Chain K: P.15, Y.16, R.133 Chain L: W.149, R.150 Ligands: 4NC.86 Ligand excluded by PLIP BME.77: 4 residues within 4Å: Chain L: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.78: 3 residues within 4Å: Chain L: H.234, F.235 Chain P: S.138 Ligand excluded by PLIP BME.79: 3 residues within 4Å: Chain L: R.107, P.118, L.119 Ligand excluded by PLIP BME.80: 1 residues within 4Å: Chain L: R.83 Ligand excluded by PLIP BME.81: 3 residues within 4Å: Chain J: P.22, I.28 Chain L: R.33 Ligand excluded by PLIP BME.89: 3 residues within 4Å: Chain M: P.42, H.48, K.180 Ligand excluded by PLIP BME.90: 6 residues within 4Å: Chain M: L.23, N.28, P.29 Chain N: N.66, F.67, V.126 Ligand excluded by PLIP BME.96: 3 residues within 4Å: Chain N: F.56, C.129, L.130 Ligand excluded by PLIP BME.97: 2 residues within 4Å: Chain N: D.132, S.133 Ligand excluded by PLIP BME.98: 6 residues within 4Å: Chain N: R.150, P.153 Chain P: S.38, I.39, P.40 Chain T: P.215 Ligand excluded by PLIP BME.103: 4 residues within 4Å: Chain O: N.152, A.153, P.164, R.167 Ligand excluded by PLIP BME.109: 3 residues within 4Å: Chain P: H.234, F.235 Chain T: H.61 Ligand excluded by PLIP BME.111: 5 residues within 4Å: Chain P: R.7, F.8, R.231 Chain T: A.213, P.215 Ligand excluded by PLIP BME.117: 6 residues within 4Å: Chain Q: N.152, A.153, L.158, N.159, R.167, E.168 Ligand excluded by PLIP BME.118: 6 residues within 4Å: Chain Q: P.15, Y.16, R.133 Chain R: W.149, R.150 Ligands: 4NC.129 Ligand excluded by PLIP BME.120: 4 residues within 4Å: Chain R: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.121: 3 residues within 4Å: Chain J: S.138 Chain R: H.234, F.235 Ligand excluded by PLIP BME.122: 3 residues within 4Å: Chain R: R.107, P.118, L.119 Ligand excluded by PLIP BME.123: 1 residues within 4Å: Chain R: R.83 Ligand excluded by PLIP BME.124: 3 residues within 4Å: Chain P: P.22, I.28 Chain R: R.33 Ligand excluded by PLIP BME.132: 3 residues within 4Å: Chain S: P.42, H.48, K.180 Ligand excluded by PLIP BME.133: 6 residues within 4Å: Chain S: L.23, N.28, P.29 Chain T: N.66, F.67, V.126 Ligand excluded by PLIP BME.139: 3 residues within 4Å: Chain T: F.56, C.129, L.130 Ligand excluded by PLIP BME.140: 2 residues within 4Å: Chain T: D.132, S.133 Ligand excluded by PLIP BME.141: 6 residues within 4Å: Chain N: P.215 Chain T: R.150, P.153 Chain V: S.38, I.39, P.40 Ligand excluded by PLIP BME.146: 4 residues within 4Å: Chain U: N.152, A.153, P.164, R.167 Ligand excluded by PLIP BME.152: 3 residues within 4Å: Chain N: H.61 Chain V: H.234, F.235 Ligand excluded by PLIP BME.154: 5 residues within 4Å: Chain N: A.213, P.215 Chain V: R.7, F.8, R.231 Ligand excluded by PLIP BME.160: 6 residues within 4Å: Chain W: N.152, A.153, L.158, N.159, R.167, E.168 Ligand excluded by PLIP BME.161: 6 residues within 4Å: Chain W: P.15, Y.16, R.133 Chain X: W.149, R.150 Ligands: 4NC.172 Ligand excluded by PLIP BME.163: 4 residues within 4Å: Chain X: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.164: 3 residues within 4Å: Chain D: S.138 Chain X: H.234, F.235 Ligand excluded by PLIP BME.165: 3 residues within 4Å: Chain X: R.107, P.118, L.119 Ligand excluded by PLIP BME.166: 1 residues within 4Å: Chain X: R.83 Ligand excluded by PLIP BME.167: 3 residues within 4Å: Chain V: P.22, I.28 Chain X: R.33 Ligand excluded by PLIP

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

TRS.5: 7 residues within 4Å: Chain A: T.169, I.171, K.173, R.184, F.185, D.186, R.188 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.168, A:I.171, A:D.186, A:D.186, A:R.188 Water bridges: A:D.186, A:R.188 TRS.18: 7 residues within 4Å: Chain C: E.168, T.169, I.171, R.184, F.185, D.186, R.188 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.169, C:D.186, C:R.188, C:R.188 Water bridges: C:E.168, C:I.171, C:G.193 TRS.39: 7 residues within 4Å: Chain F: Q.203, I.205, A.206, K.207, R.222, F.223, D.224 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.222, F:D.224 TRS.48: 7 residues within 4Å: Chain G: T.169, I.171, K.173, R.184, F.185, D.186, R.188 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:E.168, G:I.171, G:D.186, G:D.186, G:R.188 Water bridges: G:D.186, G:R.188 TRS.61: 7 residues within 4Å: Chain I: E.168, T.169, I.171, R.184, F.185, D.186, R.188 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:T.169, I:D.186, I:R.188, I:R.188 Water bridges: I:E.168, I:I.171, I:G.193 TRS.82: 7 residues within 4Å: Chain L: Q.203, I.205, A.206, K.207, R.222, F.223, D.224 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.222, L:D.224 TRS.91: 7 residues within 4Å: Chain M: T.169, I.171, K.173, R.184, F.185, D.186, R.188 6 PLIP interactions: 6 interactions with chain M Hydrogen bonds: M:E.168, M:I.171, M:D.186, M:D.186, M:R.188 Water bridges: M:R.188 TRS.104: 7 residues within 4Å: Chain O: E.168, T.169, I.171, R.184, F.185, D.186, R.188 7 PLIP interactions: 7 interactions with chain O Hydrogen bonds: O:T.169, O:D.186, O:R.188, O:R.188 Water bridges: O:E.168, O:I.171, O:G.193 TRS.125: 7 residues within 4Å: Chain R: Q.203, I.205, A.206, K.207, R.222, F.223, D.224 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:R.222, R:D.224 TRS.134: 7 residues within 4Å: Chain S: T.169, I.171, K.173, R.184, F.185, D.186, R.188 6 PLIP interactions: 6 interactions with chain S Hydrogen bonds: S:E.168, S:I.171, S:D.186, S:D.186, S:R.188 Water bridges: S:R.188 TRS.147: 7 residues within 4Å: Chain U: E.168, T.169, I.171, R.184, F.185, D.186, R.188 7 PLIP interactions: 7 interactions with chain U Hydrogen bonds: U:T.169, U:D.186, U:R.188, U:R.188 Water bridges: U:E.168, U:I.171, U:G.193 TRS.168: 7 residues within 4Å: Chain X: Q.203, I.205, A.206, K.207, R.222, F.223, D.224 2 PLIP interactions: 2 interactions with chain X Hydrogen bonds: X:R.222, X:D.224

20 x CO3: CARBONATE ION(Non-functional Binders)

CO3.6: 3 residues within 4Å: Chain A: Y.56, G.60, R.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.60, A:R.188, A:R.188 CO3.13: 1 residues within 4Å: Chain B: R.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.83 CO3.14: 3 residues within 4Å: Chain B: T.233, H.234, F.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.235 CO3.27: 6 residues within 4Å: Chain D: R.150, G.152, P.153 Chain F: S.38, I.39, P.40 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:P.153 Water bridges: F:S.38 CO3.33: 9 residues within 4Å: Chain E: R.38, L.39, A.40, K.41, N.84, L.85, N.87, A.88, N.90 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.38, E:L.85 Water bridges: E:N.90 CO3.49: 3 residues within 4Å: Chain G: Y.56, G.60, R.188 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.60, G:R.188, G:R.188 CO3.56: 1 residues within 4Å: Chain H: R.83 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.83 CO3.57: 3 residues within 4Å: Chain H: T.233, H.234, F.235 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:F.235 CO3.70: 6 residues within 4Å: Chain J: R.150, G.152, P.153 Chain L: S.38, I.39, P.40 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain L Hydrogen bonds: J:P.153 Water bridges: L:S.38 CO3.76: 9 residues within 4Å: Chain K: R.38, L.39, A.40, K.41, N.84, L.85, N.87, A.88, N.90 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:R.38, K:L.85 Water bridges: K:N.90 CO3.92: 3 residues within 4Å: Chain M: Y.56, G.60, R.188 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:G.60, M:R.188, M:R.188 CO3.99: 1 residues within 4Å: Chain N: R.83 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:R.83 CO3.100: 3 residues within 4Å: Chain N: T.233, H.234, F.235 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:F.235 Water bridges: N:T.233 CO3.113: 6 residues within 4Å: Chain P: R.150, G.152, P.153 Chain R: S.38, I.39, P.40 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain P Water bridges: R:S.38 Hydrogen bonds: P:P.153 CO3.119: 9 residues within 4Å: Chain Q: R.38, L.39, A.40, K.41, N.84, L.85, N.87, A.88, N.90 3 PLIP interactions: 3 interactions with chain Q Hydrogen bonds: Q:R.38, Q:L.85 Water bridges: Q:N.90 CO3.135: 3 residues within 4Å: Chain S: Y.56, G.60, R.188 3 PLIP interactions: 3 interactions with chain S Hydrogen bonds: S:G.60, S:R.188, S:R.188 CO3.142: 1 residues within 4Å: Chain T: R.83 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:R.83 CO3.143: 3 residues within 4Å: Chain T: T.233, H.234, F.235 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:F.235 Water bridges: T:T.233 CO3.156: 6 residues within 4Å: Chain V: R.150, G.152, P.153 Chain X: S.38, I.39, P.40 2 PLIP interactions: 1 interactions with chain V, 1 interactions with chain X Hydrogen bonds: V:P.153 Water bridges: X:S.38 CO3.162: 9 residues within 4Å: Chain W: R.38, L.39, A.40, K.41, N.84, L.85, N.87, A.88, N.90 3 PLIP interactions: 3 interactions with chain W Hydrogen bonds: W:R.38, W:L.85 Water bridges: W:N.90

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

FE.7: 4 residues within 4Å: Chain B: Y.108, H.160, H.162 Ligands: 4NC.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.108, B:H.160, B:H.162, H2O.14 FE.24: 4 residues within 4Å: Chain D: Y.108, H.160, H.162 Ligands: 4NC.26 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.108, D:H.160, D:H.162, H2O.28 FE.42: 4 residues within 4Å: Chain F: Y.108, H.160, H.162 Ligands: 4NC.43 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:Y.108, F:H.160, F:H.162, H2O.40 FE.50: 4 residues within 4Å: Chain H: Y.108, H.160, H.162 Ligands: 4NC.58 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:Y.108, H:H.160, H:H.162, H2O.55 FE.67: 4 residues within 4Å: Chain J: Y.108, H.160, H.162 Ligands: 4NC.69 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:Y.108, J:H.160, J:H.162, H2O.69 FE.85: 4 residues within 4Å: Chain L: Y.108, H.160, H.162 Ligands: 4NC.86 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:Y.108, L:H.160, L:H.162, H2O.81 FE.93: 4 residues within 4Å: Chain N: Y.108, H.160, H.162 Ligands: 4NC.101 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:Y.108, N:H.160, N:H.162, H2O.96 FE.110: 4 residues within 4Å: Chain P: Y.108, H.160, H.162 Ligands: 4NC.112 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:Y.108, P:H.160, P:H.162, H2O.110 FE.128: 4 residues within 4Å: Chain R: Y.108, H.160, H.162 Ligands: 4NC.129 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:Y.108, R:H.160, R:H.162, H2O.122 FE.136: 4 residues within 4Å: Chain T: Y.108, H.160, H.162 Ligands: 4NC.144 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:Y.108, T:H.160, T:H.162, H2O.137 FE.153: 4 residues within 4Å: Chain V: Y.108, H.160, H.162 Ligands: 4NC.155 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:Y.108, V:H.160, V:H.162, H2O.151 FE.171: 4 residues within 4Å: Chain X: Y.108, H.160, H.162 Ligands: 4NC.172 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:Y.108, X:H.160, X:H.162, H2O.163

16 x 4NC: 4-NITROCATECHOL(Non-covalent)

4NC.15: 14 residues within 4Å: Chain A: T.12, G.14, P.15, R.133 Chain B: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.7 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.149, B:R.157, B:I.191, A:P.15 Hydrogen bonds: B:R.157, B:Q.177 4NC.26: 14 residues within 4Å: Chain C: T.12, G.14, P.15, R.133 Chain D: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.24 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.149, D:R.157, D:I.191 Hydrogen bonds: D:R.157, D:Q.177 4NC.41: 7 residues within 4Å: Chain F: I.186, P.187, K.193, P.198, V.201, Q.202, I.205 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:I.186, F:V.201, F:I.205 Hydrogen bonds: F:Q.202 4NC.43: 15 residues within 4Å: Chain E: T.12, G.14, P.15, R.133 Chain F: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: BME.32, FE.42 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:W.149, F:R.157, F:I.191, E:P.15 Hydrogen bonds: F:R.157, F:Q.177 4NC.58: 14 residues within 4Å: Chain G: T.12, G.14, P.15, R.133 Chain H: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.50 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:W.149, H:R.157, H:I.191, G:P.15 Hydrogen bonds: H:R.157, H:Q.177 4NC.69: 14 residues within 4Å: Chain I: T.12, G.14, P.15, R.133 Chain J: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.67 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:W.149, J:R.157, J:I.191 Hydrogen bonds: J:R.157, J:Q.177 4NC.84: 7 residues within 4Å: Chain L: I.186, P.187, K.193, P.198, V.201, Q.202, I.205 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:I.186, L:V.201, L:I.205 Hydrogen bonds: L:Q.202 4NC.86: 15 residues within 4Å: Chain K: T.12, G.14, P.15, R.133 Chain L: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: BME.75, FE.85 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: L:W.149, L:R.157, L:I.191, K:P.15 Hydrogen bonds: L:R.157, L:Q.177 4NC.101: 14 residues within 4Å: Chain M: T.12, G.14, P.15, R.133 Chain N: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.93 6 PLIP interactions: 5 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:W.149, N:R.157, N:I.191, M:P.15 Hydrogen bonds: N:R.157, N:Q.177 4NC.112: 14 residues within 4Å: Chain O: T.12, G.14, P.15, R.133 Chain P: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.110 5 PLIP interactions: 5 interactions with chain P Hydrophobic interactions: P:W.149, P:R.157, P:I.191 Hydrogen bonds: P:R.157, P:Q.177 4NC.127: 7 residues within 4Å: Chain R: I.186, P.187, K.193, P.198, V.201, Q.202, I.205 4 PLIP interactions: 4 interactions with chain R Hydrophobic interactions: R:I.186, R:V.201, R:I.205 Hydrogen bonds: R:Q.202 4NC.129: 15 residues within 4Å: Chain Q: T.12, G.14, P.15, R.133 Chain R: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: BME.118, FE.128 6 PLIP interactions: 5 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: R:W.149, R:R.157, R:I.191, Q:P.15 Hydrogen bonds: R:R.157, R:Q.177 4NC.144: 14 residues within 4Å: Chain S: T.12, G.14, P.15, R.133 Chain T: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.136 6 PLIP interactions: 5 interactions with chain T, 1 interactions with chain S Hydrophobic interactions: T:W.149, T:R.157, T:I.191, S:P.15 Hydrogen bonds: T:R.157, T:Q.177 4NC.155: 14 residues within 4Å: Chain U: T.12, G.14, P.15, R.133 Chain V: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.153 5 PLIP interactions: 5 interactions with chain V Hydrophobic interactions: V:W.149, V:R.157, V:I.191 Hydrogen bonds: V:R.157, V:Q.177 4NC.170: 7 residues within 4Å: Chain X: I.186, P.187, K.193, P.198, V.201, Q.202, I.205 4 PLIP interactions: 4 interactions with chain X Hydrophobic interactions: X:I.186, X:V.201, X:I.205 Hydrogen bonds: X:Q.202 4NC.172: 15 residues within 4Å: Chain W: T.12, G.14, P.15, R.133 Chain X: Y.24, Y.108, H.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: BME.161, FE.171 6 PLIP interactions: 5 interactions with chain X, 1 interactions with chain W Hydrophobic interactions: X:W.149, X:R.157, X:I.191, W:P.15 Hydrogen bonds: X:R.157, X:Q.177

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

CL.19: 3 residues within 4Å: Chain C: H.61, L.62, R.64 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain D: A.58, H.59, H.61, D.62 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain F: D.132, S.133 Ligand excluded by PLIP CL.62: 3 residues within 4Å: Chain I: H.61, L.62, R.64 Ligand excluded by PLIP CL.71: 4 residues within 4Å: Chain J: A.58, H.59, H.61, D.62 Ligand excluded by PLIP CL.83: 2 residues within 4Å: Chain L: D.132, S.133 Ligand excluded by PLIP CL.105: 3 residues within 4Å: Chain O: H.61, L.62, R.64 Ligand excluded by PLIP CL.114: 4 residues within 4Å: Chain P: A.58, H.59, H.61, D.62 Ligand excluded by PLIP CL.126: 2 residues within 4Å: Chain R: D.132, S.133 Ligand excluded by PLIP CL.148: 3 residues within 4Å: Chain U: H.61, L.62, R.64 Ligand excluded by PLIP CL.157: 4 residues within 4Å: Chain V: A.58, H.59, H.61, D.62 Ligand excluded by PLIP CL.169: 2 residues within 4Å: Chain X: D.132, S.133 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purpero, V.M. et al., Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis. To be Published (2010)

Release Date

2011-03-09

Peptides

Protocatechuate 3,4-dioxygenase alpha chain: ACEGIKMOQSUW
Protocatechuate 3,4-dioxygenase beta chain: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
A

I
B

K
C

M
A

O
B

Q
C

S
A

U
B

W
C

B
M

D
N

F
O

H
M

J
N

L
O

N
M

P
N

R
O

T
M

V
N

X
O

Protocatechuate 3,4-dioxygenase alpha chain

Protocatechuate 3,4-dioxygenase beta chain

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