SMTL ID : 5axo.1

Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Meropenem

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.72, H.74, H.77, H.150 Ligands: ZN.2, LMP.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:H.74, A:H.150, H2O.3 ZN.2: 5 residues within 4Å: Chain A: D.76, H.77, H.215 Ligands: ZN.1, LMP.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.76, A:H.77, A:H.215, H2O.3

10 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: P.8, Q.9, V.50, N.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.9, A:N.54 NA.4: 6 residues within 4Å: Chain A: R.3, G.24, G.25, P.216, E.217, W.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.217, A:W.222 NA.5: 3 residues within 4Å: Chain A: I.245, A.248, G.249 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.248 NA.6: 4 residues within 4Å: Chain A: P.112, H.150, T.177, V.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.150, A:V.179 Water bridges: A:Q.113 NA.7: 5 residues within 4Å: Chain A: S.82, Q.85, K.86, S.123, A.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.82, A:A.124 NA.8: 6 residues within 4Å: Chain A: R.103, A.124, K.125, V.126, R.127 Ligands: SO4.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.103, A:S.123, A:K.125, A:V.126, A:R.127 NA.9: 2 residues within 4Å: Chain A: S.234, V.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.234 Water bridges: A:S.234 NA.10: 6 residues within 4Å: Chain A: S.70, T.71, A.94, G.95, G.153, I.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.71, A:G.95, A:I.155 Water bridges: A:N.98 NA.11: 5 residues within 4Å: Chain A: S.73, A.97, N.98, T.101, P.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.73, A:S.73 Water bridges: A:T.101, A:E.152 NA.12: 4 residues within 4Å: Chain A: G.16, N.17, H.19, S.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.16, A:S.32

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

SO4.13: 3 residues within 4Å: Chain A: T.177, R.252 Ligands: TRS.16 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.248, A:R.252 Salt bridges: A:R.252 SO4.14: 4 residues within 4Å: Chain A: A.124, K.125, R.127 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125 Salt bridges: A:R.127 SO4.15: 4 residues within 4Å: Chain A: R.56, K.61, L.62, S.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.62, A:S.63 Water bridges: A:S.63 Salt bridges: A:R.56

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.16: 4 residues within 4Å: Chain A: E.217, V.218, D.220 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.218, A:D.220

1 x LMP: (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid(Non-covalent)

LMP.17: 15 residues within 4Å: Chain A: W.5, H.72, H.74, D.76, H.77, Q.113, L.117, H.150, S.175, T.177, H.215, E.217, R.252 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.5, A:L.117 Hydrogen bonds: A:H.74, A:Q.113, A:S.175 Water bridges: A:W.5, A:H.72, A:H.77 Salt bridges: A:H.72, A:H.77, A:H.150, A:H.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wachino, J. et al., Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Meropenem. To Be Published

Release Date

2016-05-11

Peptides

Metallo-beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase

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