SMTL ID : 3qnc.1

Crystal Structure of a Rationally Designed OXA-10 Variant Showing Carbapenemase Activity, OXA-10loop48

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: S.48, S.96, K.186, T.187, G.188, Y.189, R.228 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.48, A:S.96, A:S.96, A:T.187, A:T.187 Water bridges: A:S.96, A:Y.189, A:R.228, A:R.228 Salt bridges: A:K.186, A:R.228 SO4.2: 2 residues within 4Å: Chain A: K.115, K.119 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.119 Salt bridges: A:K.115, A:K.119 SO4.3: 2 residues within 4Å: Chain A: G.1, K.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.1 Water bridges: A:S.29 Salt bridges: A:K.30 SO4.4: 2 residues within 4Å: Chain A: R.141 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.141 SO4.5: 3 residues within 4Å: Chain A: L.136, T.191, R.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.191 Water bridges: A:Y.189, A:R.192 Salt bridges: A:R.192 SO4.6: 7 residues within 4Å: Chain A: E.180, E.205, K.206, E.207 Chain B: T.88, R.90, G.91 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.205, B:G.91 Salt bridges: B:R.90 SO4.14: 7 residues within 4Å: Chain B: S.48, S.96, K.186, T.187, G.188, Y.189, R.228 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.48, B:S.96, B:T.187, B:T.187 Water bridges: B:K.186, B:Y.189, B:R.228, B:R.228 Salt bridges: B:K.186, B:R.228 SO4.15: 4 residues within 4Å: Chain B: T.61, R.112, K.115, Y.116 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.112, B:Y.116 Salt bridges: B:R.112, B:K.115 SO4.16: 2 residues within 4Å: Chain B: R.141, I.193 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.43, B:E.43, B:R.141 Salt bridges: B:R.141

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: T.88, R.90 Chain B: E.180, Y.181, E.205, E.207 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.88, A:T.88, A:R.90 Water bridges: B:K.206 EDO.8: 6 residues within 4Å: Chain A: L.156, N.157, K.163 Chain B: N.66, E.67, H.68 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.157, A:K.163 Water bridges: B:N.66, B:N.66 EDO.9: 2 residues within 4Å: Chain A: S.162, K.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.163 Water bridges: A:E.164 EDO.10: 7 residues within 4Å: Chain A: Y.44, L.45, R.141, I.193, E.194, P.195 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.45, A:E.194 Water bridges: A:S.190 EDO.11: 2 residues within 4Å: Chain A: K.76, P.77 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: S.128, G.129, G.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.129, A:G.130 Water bridges: A:S.128 EDO.17: 3 residues within 4Å: Chain B: G.109, E.110, V.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.111 Water bridges: B:R.112 EDO.18: 4 residues within 4Å: Chain B: N.19, G.20, R.39, K.42 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.39, B:K.42, B:K.42 Water bridges: B:G.20

1 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.13: 6 residues within 4Å: Chain A: R.39, K.42, Y.44, P.195, I.197, D.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.39, A:R.39, A:K.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Luca, F. et al., Evolution to carbapenem-hydrolyzing activity in noncarbapenemase class D {beta}-lactamase OXA-10 by rational protein design. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-11-02

Peptides

Oxacillinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Oxacillinase

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