SMTL ID : 5ypn.1 (1 other biounit)

Crystal structure of NDM-1 bound to hydrolyzed meropenem representing an EI2 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: LMP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.2: 4 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: LMP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.96, A:D.96, A:C.180, A:H.222

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.3: 14 residues within 4Å: Chain A: V.45, W.65, H.92, H.94, Q.95, D.96, H.161, C.180, K.183, G.191, N.192, H.222 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.45, A:W.65 Hydrogen bonds: A:D.96, A:D.96, A:N.192, A:N.192 Salt bridges: A:H.92, A:H.94, A:H.161, A:H.161, A:K.183, A:H.222

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

SO4.4: 3 residues within 4Å: Chain A: R.206, T.232, R.236 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.206, A:R.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, H. et al., The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis. Nat Commun (2017)

Release Date

2018-02-21

Peptides

Metallo-beta-lactamase NDM-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase NDM-1

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