SMTL ID : 8qnz.1

OXA-48 with carbamylated Lys73 in complex with hydrolysed Imipenem and bromide ion competing for binding with Arg250 at neutral pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-tetramer

Ligands

3 x 8YF: (2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid(Non-covalent)

8YF.1: 17 residues within 4Å: Chain A: A.64, S.65, K.68, I.97, W.100, S.113, V.115, L.153, K.203, T.204, G.205, Y.206, T.208, S.239, L.242, R.245 Ligands: BR.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.65, A:S.65, A:S.65, A:S.113, A:T.204, A:Y.206 Water bridges: A:R.209, A:R.245, A:R.245 Salt bridges: A:K.203, A:R.245 8YF.7: 17 residues within 4Å: Chain B: A.64, S.65, K.68, I.97, W.100, S.113, V.115, L.153, K.203, T.204, G.205, Y.206, T.208, S.239, L.242, R.245 Ligands: BR.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.65, B:S.65, B:S.65, B:S.113, B:T.204, B:Y.206 Water bridges: B:S.113, B:T.208, B:R.245 Salt bridges: B:K.203, B:R.245 8YF.14: 17 residues within 4Å: Chain D: A.64, S.65, K.68, I.97, W.100, S.113, V.115, L.153, K.203, T.204, G.205, Y.206, T.208, S.239, L.242, R.245 Ligands: BR.15 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:T.208 Hydrogen bonds: D:S.65, D:S.65, D:S.65, D:S.113, D:T.204, D:Y.206 Water bridges: D:R.245, D:R.245, D:R.245 Salt bridges: D:K.203, D:R.245

11 x BR: BROMIDE ION(Non-covalent)

BR.2: 6 residues within 4Å: Chain A: Q.188, L.191, R.201 Chain D: Q.188, L.191, R.201 Ligand excluded by PLIP BR.3: 5 residues within 4Å: Chain A: R.181, R.184 Chain D: E.180, R.181, R.184 Ligand excluded by PLIP BR.4: 1 residues within 4Å: Chain A: R.129 Ligand excluded by PLIP BR.5: 4 residues within 4Å: Chain A: R.169, K.170, H.173, K.175 Ligand excluded by PLIP BR.6: 7 residues within 4Å: Chain A: S.65, S.113, T.204, G.205, Y.206, R.245 Ligands: 8YF.1 Ligand excluded by PLIP BR.9: 6 residues within 4Å: Chain B: Q.188, L.191, R.201 Chain C: Q.188, L.191, R.201 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain B: K.132, M.133, H.177 Ligand excluded by PLIP BR.11: 7 residues within 4Å: Chain B: S.65, S.113, T.204, G.205, Y.206, R.245 Ligands: 8YF.7 Ligand excluded by PLIP BR.12: 5 residues within 4Å: Chain B: E.180, R.181, R.184 Chain C: R.181, R.184 Ligand excluded by PLIP BR.13: 7 residues within 4Å: Chain C: S.65, S.113, K.203, T.204, G.205, Y.206, R.245 Ligand excluded by PLIP BR.15: 7 residues within 4Å: Chain D: S.65, S.113, T.204, G.205, Y.206, R.245 Ligands: 8YF.14 Ligand excluded by PLIP

1 x 1BO: 1-BUTANOL(Non-covalent)

1BO.8: 5 residues within 4Å: Chain A: N.147 Chain B: R.123, G.126, V.148, D.149 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.123, B:R.123, B:V.148 Water bridges: B:R.123, B:Q.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Q. et al., An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity. Acs Cent.Sci. (2023)

Release Date

2023-11-08

Peptides

Beta-lactamase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

Beta-lactamase

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