SMTL ID : 3pnz.8 (7 other biounits)

Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: E.209, Y.210, R.324, T.327, K.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.209, A:T.327 Water bridges: A:T.327, A:K.329 GOL.2: 5 residues within 4Å: Chain A: F.18, L.58, G.59, A.292, V.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.58 Water bridges: A:G.59 GOL.3: 5 residues within 4Å: Chain A: Y.223, K.226, Q.227, K.230 Chain C: E.305 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.223, A:Q.227, A:K.230, A:K.230 GOL.9: 5 residues within 4Å: Chain B: Y.8, L.76, A.79, Q.80, Y.148 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.148 GOL.10: 7 residues within 4Å: Chain B: I.240, A.241, G.271, T.273, Y.278, P.286, G.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.273, B:G.287 GOL.11: 6 residues within 4Å: Chain B: Y.8, S.82, K.83, G.86, I.87, Q.88 No protein-ligand interaction detected (PLIP) GOL.17: 7 residues within 4Å: Chain C: I.240, A.241, G.271, T.273, Y.278, P.286, G.287 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.273, C:G.287 Water bridges: C:T.273 GOL.18: 4 residues within 4Å: Chain C: V.26, D.43, R.74, D.77 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.74, C:D.77 Water bridges: C:K.45, C:R.74 GOL.19: 2 residues within 4Å: Chain C: K.226, K.230 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.226, C:K.230 Water bridges: C:K.230, C:E.261, B:E.305, B:E.305, B:E.305 GOL.20: 3 residues within 4Å: Chain C: I.198, K.202, T.231 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.202

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: H.22, H.24, K.154, D.272 Ligands: ZN.5, PO4.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.22, A:H.24, A:D.272 ZN.5: 6 residues within 4Å: Chain A: N.96, K.154, H.187, H.215 Ligands: ZN.4, PO4.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.187, A:H.215 ZN.12: 6 residues within 4Å: Chain B: H.22, H.24, K.154, D.272 Ligands: ZN.13, PO4.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.22, B:H.24, B:D.272 ZN.13: 6 residues within 4Å: Chain B: H.22, K.154, H.187, H.215 Ligands: ZN.12, PO4.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.187, B:H.215 ZN.21: 6 residues within 4Å: Chain C: H.22, H.24, K.154, D.272 Ligands: ZN.22, PO4.23 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.22, C:H.24, C:D.272 ZN.22: 7 residues within 4Å: Chain C: H.22, N.96, K.154, H.187, H.215 Ligands: ZN.21, PO4.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.187, C:H.215

11 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 11 residues within 4Å: Chain A: H.22, H.24, Y.71, N.96, K.97, K.154, H.187, H.215, D.272 Ligands: ZN.4, ZN.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.96 Water bridges: A:Y.71 Salt bridges: A:H.24, A:K.97, A:H.187, A:H.215 PO4.7: 5 residues within 4Å: Chain A: K.242, K.244, Y.245, R.275, Y.278 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.245, A:Y.278, A:Y.278 Water bridges: A:Y.245, A:D.272, A:D.272, A:R.275, A:R.275 Salt bridges: A:K.242, A:K.244, A:R.275 PO4.8: 3 residues within 4Å: Chain A: T.127, T.128, K.168 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.128, A:T.128 Water bridges: A:D.129, A:D.129, A:K.168 Salt bridges: A:K.168 PO4.14: 11 residues within 4Å: Chain B: H.22, H.24, Y.71, N.96, K.97, K.154, H.187, H.215, D.272 Ligands: ZN.12, ZN.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.96, B:N.96 Water bridges: B:Y.71, B:K.97 Salt bridges: B:H.24, B:K.97, B:H.187, B:H.215 PO4.15: 5 residues within 4Å: Chain B: K.242, K.244, Y.245, R.275, Y.278 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.278, B:Y.278 Water bridges: B:K.242, B:K.242, B:Y.245, B:R.275 Salt bridges: B:K.242, B:K.244, B:R.275 PO4.16: 2 residues within 4Å: Chain B: T.127, T.128 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.128, B:T.128 Water bridges: B:T.127, B:D.129, B:K.168 Salt bridges: B:K.168 PO4.23: 11 residues within 4Å: Chain C: H.22, H.24, Y.71, N.96, K.97, K.154, H.187, H.215, D.272 Ligands: ZN.21, ZN.22 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.96, C:N.96 Water bridges: C:Y.71, C:Y.71, C:K.97, C:K.97 Salt bridges: C:H.24, C:K.97, C:H.187, C:H.215 PO4.24: 5 residues within 4Å: Chain C: K.242, K.244, Y.245, R.275, Y.278 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.278 Water bridges: C:K.244, C:Y.245, C:Y.245 Salt bridges: C:K.242, C:K.244, C:R.275 PO4.25: 2 residues within 4Å: Chain C: T.127, T.128 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.128 Water bridges: C:T.127, C:D.129, C:K.168 Salt bridges: C:K.168 PO4.26: 6 residues within 4Å: Chain C: Y.8, S.82, K.83, G.86, I.87, Q.88 4 PLIP interactions: 4 interactions with chain C Water bridges: C:Y.8, C:K.83, C:G.86, C:Q.88 PO4.27: 2 residues within 4Å: Chain C: K.312, K.316 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.312, C:K.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes. To be Published

Release Date

2011-11-23

Peptides

Phosphotriesterase family protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

Phosphotriesterase family protein

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