SMTL ID : 6pxx.1

Class D beta-lactamase in complex with beta-lactam antibiotic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x 5R7: (2~{S},3~{R})-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid(Covalent)

5R7.1: 11 residues within 4Å: Chain A: A.69, S.70, I.102, W.105, S.118, V.120, L.158, G.210, Y.211, S.244, R.250 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.102, A:V.120, A:L.158, A:Y.211 Hydrogen bonds: A:S.70, A:S.118, A:Y.211, A:S.244 Water bridges: A:T.209, A:R.250, A:R.250 Salt bridges: A:R.250 5R7.7: 14 residues within 4Å: Chain B: A.69, S.70, I.102, W.105, S.118, V.120, L.158, T.209, G.210, Y.211, S.244, L.247, R.250 Ligands: EPE.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.102, B:I.102, B:V.120, B:L.158, B:Y.211 Hydrogen bonds: B:S.70, B:S.118, B:Y.211 Water bridges: B:S.118, B:G.210, B:R.250 Salt bridges: B:R.250

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

EDO.2: 4 residues within 4Å: Chain A: Q.64, A.65, F.66, P.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.64 Water bridges: A:Q.64, A:Q.64, A:R.163, A:E.216 EDO.3: 7 residues within 4Å: Chain A: D.229, D.230 Chain B: V.92, D.108, H.109, N.110, T.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.229 EDO.4: 5 residues within 4Å: Chain A: Q.124, S.155, L.158, D.159, R.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.124, A:R.214, A:R.214 EDO.5: 8 residues within 4Å: Chain A: H.38, K.39, S.40, M.239, D.240, M.241, P.242, L.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.39, A:S.40 Water bridges: A:D.240 EDO.9: 7 residues within 4Å: Chain A: V.92, D.108, H.109, N.110, T.113 Chain B: D.229, D.230 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.229 Water bridges: A:D.108

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: R.206 Chain B: R.206 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: S.70, V.120, Y.123, W.157 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 7 residues within 4Å: Chain B: D.101, I.102, W.105, V.120, T.213, R.214 Ligands: 5R7.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.213 Water bridges: B:T.213, B:R.214, B:R.214, B:R.214 Salt bridges: B:D.101, B:D.101, B:R.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Papp-Wallace, K.M. et al., Structural Analysis of The OXA-48 Carbapenemase Bound to A "Poor" Carbapenem Substrate, Doripenem. Antibiotics (2019)

Release Date

2019-10-09

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase