SMTL ID : 1p9e.2 (1 other biounit)

Crystal Structure Analysis of Methyl Parathion Hydrolase from Pseudomonas sp WBC-3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.151, H.152, D.255, H.302 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.151, A:H.152, A:D.255, A:H.302, H2O.1 ZN.2: 5 residues within 4Å: Chain A: H.147, H.149, H.234, D.255 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.147, A:H.149, A:H.234, H2O.1, H2O.4 ZN.8: 5 residues within 4Å: Chain B: D.151, H.152, D.255, H.302 Ligands: CD.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.151, B:H.152, B:D.255, B:H.302, H2O.5 ZN.14: 5 residues within 4Å: Chain C: D.151, H.152, D.255, H.302 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.151, C:H.152, C:D.255, C:H.302, H2O.7 ZN.15: 5 residues within 4Å: Chain C: H.147, H.149, H.234, D.255 Ligands: ZN.14 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.147, C:H.149, C:H.234, H2O.7, H2O.11 ZN.21: 5 residues within 4Å: Chain D: D.151, H.152, D.255, H.302 Ligands: CD.22 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.151, D:H.152, D:D.255, D:H.302, H2O.12

8 x K: POTASSIUM ION(Non-covalent)

K.3: 2 residues within 4Å: Chain A: E.142 Ligands: NA.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.142, A:E.142, H2O.2 K.4: 4 residues within 4Å: Chain A: D.172, K.174, G.218, H.232 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.172, A:D.172, A:H.232, H2O.2 K.5: 2 residues within 4Å: Chain A: Q.136, E.138 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.138, A:E.138, H2O.2 K.10: 1 residues within 4Å: Chain B: D.54 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.54 K.16: 2 residues within 4Å: Chain C: E.142 Ligands: NA.19 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.142, C:E.142, H2O.9 K.17: 4 residues within 4Å: Chain C: D.172, K.174, G.218, H.232 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.172, C:D.172, C:H.232, H2O.9 K.18: 2 residues within 4Å: Chain C: Q.136, E.138 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.138, C:E.138, H2O.9 K.23: 1 residues within 4Å: Chain D: D.54 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.54

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

NA.6: 4 residues within 4Å: Chain A: V.168, R.170, K.214 Ligands: K.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.214 NA.7: 1 residues within 4Å: Chain A: E.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.247 NA.11: 2 residues within 4Å: Chain B: Q.136, E.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.136 NA.12: 3 residues within 4Å: Chain B: K.174, H.232 Chain D: K.174 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.174, B:K.174, B:H.232 NA.13: 3 residues within 4Å: Chain B: D.221, K.227 Chain D: D.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.221, B:K.227 NA.19: 4 residues within 4Å: Chain C: V.168, R.170, K.214 Ligands: K.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.170 NA.20: 1 residues within 4Å: Chain C: E.244 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.244, C:G.247 NA.24: 2 residues within 4Å: Chain D: Q.136, E.138 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.136, D:E.138 NA.25: 3 residues within 4Å: Chain B: K.174 Chain D: K.174, H.232 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174 NA.26: 3 residues within 4Å: Chain B: D.290 Chain D: D.221, K.227 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.290, D:K.227

2 x CD: CADMIUM ION(Non-covalent)

CD.9: 5 residues within 4Å: Chain B: H.147, H.149, H.234, D.255 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.147, B:H.149, B:H.234, B:D.255, H2O.4 CD.22: 5 residues within 4Å: Chain D: H.147, H.149, H.234, D.255 Ligands: ZN.21 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.147, D:H.149, D:H.234, D:D.255, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, Y. et al., Crystal Structure Analysis of Methyl Parathion Hydrolase from Pseudomonas sp WBC-3. To be Published

Release Date

2004-05-25

Peptides

Methyl Parathion Hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Methyl Parathion Hydrolase

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