SMTL ID : 3l7g.1 (2 other biounits)

Crystal structure of organophosphate anhydrolase/prolidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

3 x M44: N,N'-bis(1-methylethyl)phosphorodiamidic acid(Non-covalent)

M44.1: 13 residues within 4Å: Chain A: Y.212, L.225, D.244, D.255, H.332, H.336, V.342, H.343, E.381, R.418, E.420 Ligands: MN.2, MN.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.212, A:V.342 Hydrogen bonds: A:D.244, A:R.418 M44.6: 13 residues within 4Å: Chain B: Y.212, L.225, D.244, D.255, H.332, H.336, V.342, H.343, E.381, R.418, E.420 Ligands: MN.7, MN.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.212, B:H.332, B:V.342 Hydrogen bonds: B:D.244, B:R.418 M44.11: 14 residues within 4Å: Chain C: Y.212, L.225, H.226, D.244, D.255, H.332, H.336, V.342, H.343, E.381, R.418, E.420 Ligands: MN.12, MN.13 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.342 Hydrogen bonds: C:D.244, C:R.418

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

MN.2: 7 residues within 4Å: Chain A: D.255, H.336, T.379, E.381, E.420 Ligands: M44.1, MN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.255, A:H.336, A:E.381, A:E.420 MN.3: 6 residues within 4Å: Chain A: D.244, D.255, T.257, E.420 Ligands: M44.1, MN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.244, A:D.244, A:D.255, A:E.420 MN.4: 1 residues within 4Å: Chain A: H.226 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.226 MN.5: 2 residues within 4Å: Chain A: D.105, E.107 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.105, A:E.107 MN.7: 7 residues within 4Å: Chain B: D.255, H.336, T.379, E.381, E.420 Ligands: M44.6, MN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.255, B:H.336, B:E.381, B:E.420 MN.8: 7 residues within 4Å: Chain B: Y.212, D.244, D.255, T.257, E.420 Ligands: M44.6, MN.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.244, B:D.244, B:D.255, B:E.420, B:E.420 MN.9: 4 residues within 4Å: Chain B: R.25, E.26 Chain C: E.431, E.436 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.26, C:E.436, H2O.11 MN.10: 1 residues within 4Å: Chain B: H.226 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.226 MN.12: 7 residues within 4Å: Chain C: D.255, H.336, T.379, E.381, E.420 Ligands: M44.11, MN.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.255, C:H.336, C:E.381, C:E.420 MN.13: 6 residues within 4Å: Chain C: D.244, D.255, T.257, E.420 Ligands: M44.11, MN.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.244, C:D.244, C:D.255, C:E.420 MN.14: 1 residues within 4Å: Chain C: H.226 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.226

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

2010-02-09

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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