SMTL ID : 3l24.3 (2 other biounits)

Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

10 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: D.255, H.336, T.379, E.381, E.420 Ligands: MN.2, GOA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.255, A:H.336, A:E.381, A:E.420, GOA.4 MN.2: 7 residues within 4Å: Chain A: Y.212, D.244, D.255, T.257, E.420 Ligands: MN.1, GOA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.244, A:D.244, A:D.255, A:E.420, GOA.4 MN.3: 2 residues within 4Å: Chain A: D.105, E.107 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.105, A:E.107, H2O.5, H2O.6, H2O.6, H2O.6 MN.5: 7 residues within 4Å: Chain B: D.255, H.336, T.379, E.381, E.420 Ligands: MN.6, GOA.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.255, B:H.336, B:E.381, B:E.420, GOA.9 MN.6: 7 residues within 4Å: Chain B: Y.212, D.244, D.255, T.257, E.420 Ligands: MN.5, GOA.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.244, B:D.244, B:D.255, B:E.420, GOA.9 MN.7: 2 residues within 4Å: Chain B: E.26 Chain C: E.436 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:E.436, B:E.26, H2O.11, H2O.12, H2O.16 MN.8: 1 residues within 4Å: Chain B: H.226 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.226 MN.10: 7 residues within 4Å: Chain C: D.255, H.336, T.379, E.381, E.420 Ligands: MN.11, GOA.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.255, C:H.336, C:E.381, C:E.420, GOA.13 MN.11: 7 residues within 4Å: Chain C: Y.212, D.244, D.255, T.257, E.420 Ligands: MN.10, GOA.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.244, C:D.244, C:D.255, C:E.420, GOA.13 MN.12: 1 residues within 4Å: Chain C: H.226 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.226

3 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.4: 9 residues within 4Å: Chain A: Y.212, D.244, D.255, H.336, H.343, E.381, E.420 Ligands: MN.1, MN.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.336, A:H.343 GOA.9: 9 residues within 4Å: Chain B: Y.212, D.244, D.255, H.336, H.343, E.381, E.420 Ligands: MN.5, MN.6 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.336, B:H.343 GOA.13: 10 residues within 4Å: Chain C: Y.212, D.244, D.255, H.336, V.342, H.343, E.381, E.420 Ligands: MN.10, MN.11 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.336, C:H.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, N.K. et al., Structural insights into the dual activities of the nerve agent degrading organophosphate anhydrolase/prolidase. Biochemistry (2010)

Release Date

2010-01-26

Peptides

Xaa-Pro dipeptidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Xaa-Pro dipeptidase

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