SMTL ID : 3rhg.1

Crystal structure of amidohydrolase pmi1525 (target efi-500319) from proteus mirabilis hi4320

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.23, H.25, E.166, D.294 Ligands: ZN.2, CAC.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.23, A:H.25, A:E.166, A:D.294 ZN.2: 5 residues within 4Å: Chain A: E.166, H.199, H.229 Ligands: ZN.1, CAC.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.166, A:H.199, A:H.229 ZN.9: 6 residues within 4Å: Chain B: H.23, H.25, E.166, D.294 Ligands: ZN.10, CAC.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.23, B:H.25, B:E.166, B:D.294 ZN.10: 5 residues within 4Å: Chain B: E.166, H.199, H.229 Ligands: ZN.9, CAC.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.166, B:H.199, B:H.229

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.3: 12 residues within 4Å: Chain A: Y.63, H.199, W.203, H.229, M.254, L.257, F.261, E.264, D.294, F.296 Ligands: CAC.4, UNL.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.257, A:F.261, A:F.296 Water bridges: A:Y.63, A:G.202, A:G.202, A:E.264 Salt bridges: A:H.199 pi-Stacking: A:H.229 BEZ.11: 12 residues within 4Å: Chain B: Y.63, H.199, W.203, H.229, M.254, L.257, F.261, E.264, D.294, F.296 Ligands: CAC.12, UNL.15 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.257, B:F.261, B:F.296 Water bridges: B:Y.63, B:Y.63, B:G.202, B:G.202, B:E.264 Salt bridges: B:H.199 pi-Stacking: B:H.229

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.4: 14 residues within 4Å: Chain A: H.23, H.25, Y.126, E.166, H.199, H.229, D.294, F.296 Ligands: ZN.1, ZN.2, BEZ.3, UNL.6, UNL.7, UNL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.126 CAC.12: 14 residues within 4Å: Chain B: H.23, H.25, Y.126, E.166, H.199, H.229, D.294, F.296 Ligands: ZN.9, ZN.10, BEZ.11, UNL.14, UNL.15, UNL.16 No protein-ligand interaction detected (PLIP)

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

SO4.5: 5 residues within 4Å: Chain A: M.1, G.3, K.14, A.344, E.345 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.1, A:G.3, A:E.345 Water bridges: A:K.2, A:K.14, A:K.14 Salt bridges: A:K.14 SO4.13: 5 residues within 4Å: Chain B: M.1, G.3, K.14, A.344, E.345 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:M.1, B:M.1, B:G.3, B:E.345 Water bridges: B:K.2, B:K.14, B:K.14 Salt bridges: B:K.14

6 x UNL: UNKNOWN LIGAND

UNL.6: 7 residues within 4Å: Chain A: L.30, I.101, Y.126, F.130 Ligands: CAC.4, UNL.7, UNL.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.30, A:I.101, A:Y.126, A:F.130 UNL.7: 7 residues within 4Å: Chain A: L.30, Y.63, K.129, F.130 Ligands: BEZ.3, CAC.4, UNL.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.63, A:K.129, A:K.129, A:E.264 Salt bridges: A:K.129 UNL.8: 5 residues within 4Å: Chain A: N.28, L.30, I.101 Ligands: CAC.4, UNL.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.28, A:L.30, A:I.101 UNL.14: 7 residues within 4Å: Chain B: L.30, I.101, Y.126, F.130 Ligands: CAC.12, UNL.15, UNL.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.30, B:I.101, B:Y.126, B:F.130 Hydrogen bonds: B:Y.126 UNL.15: 7 residues within 4Å: Chain B: L.30, Y.63, K.129, F.130 Ligands: BEZ.11, CAC.12, UNL.14 7 PLIP interactions: 7 interactions with chain B Water bridges: B:Y.63, B:Y.126, B:Y.126, B:K.129, B:K.129, B:E.264 Salt bridges: B:K.129 UNL.16: 5 residues within 4Å: Chain B: N.28, L.30, I.101 Ligands: CAC.12, UNL.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.28, B:L.30, B:I.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Amidohydrolase Pmi1525 from Proteus Mirabilis Hi4320. To be Published

Release Date

2011-04-27

Peptides

Putative phophotriesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative phophotriesterase

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