SMTL ID : 4zwp.1

Crystal structure of organophosphate anhydrolase/prolidase mutant Y212F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

7 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, M44.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.255, A:H.336, A:E.381, A:E.420 MN.2: 7 residues within 4Å: Chain A: D.244, D.255, T.257, E.381, E.420 Ligands: MN.1, M44.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.244, A:D.244, A:D.255, A:E.420 MN.4: 2 residues within 4Å: Chain A: L.28, D.29 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.28, H2O.1, H2O.1 MN.5: 1 residues within 4Å: Chain A: D.29 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.29, H2O.1, H2O.4 MN.9: 6 residues within 4Å: Chain B: D.244, D.255, T.257, E.420 Ligands: MN.10, M44.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.244, B:D.244, B:D.255, B:E.420 MN.10: 6 residues within 4Å: Chain B: D.255, H.336, E.381, E.420 Ligands: MN.9, M44.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.255, B:H.336, B:E.381, B:E.420 MN.11: 1 residues within 4Å: Chain B: E.10 No protein-ligand interaction detected (PLIP)

3 x BA: BARIUM ION(Non-covalent)(Non-functional Binders)

BA.3: 1 residues within 4Å: Chain A: D.318 No protein-ligand interaction detected (PLIP) BA.6: 2 residues within 4Å: Chain A: D.309, N.311 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.309 BA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

M44.8: 14 residues within 4Å: Chain A: F.212, I.215, L.225, D.244, D.255, H.332, H.336, V.342, H.343, E.381, R.418, E.420 Ligands: MN.1, MN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.212, A:F.212, A:I.215, A:V.342 Hydrogen bonds: A:H.343 Water bridges: A:L.225 M44.12: 14 residues within 4Å: Chain B: F.212, I.215, L.225, H.226, D.244, D.255, H.332, H.336, V.342, H.343, E.381, E.420 Ligands: MN.9, MN.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.212, B:F.212, B:I.215, B:V.342 Hydrogen bonds: B:D.244, B:H.343, B:R.418

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain B: E.24, N.27, D.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.24, B:N.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daczkowski, C.M. et al., Engineering the Organophosphorus Acid Anhydrolase Enzyme for Increased Catalytic Efficiency and Broadened Stereospecificity on Russian VX. Biochemistry (2015)

Release Date

2015-10-14

Peptides

OPAA organophosphate prolidase anhydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

OPAA organophosphate prolidase anhydrolase

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