SMTL ID : 6ovz.1

Crystal structure of the New Delhi metallo-beta-lactamase-1 adduct with a lysine-targeted affinity label

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.89, C.173, H.215 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.89, A:C.173, A:H.215, H2O.4, H2O.4 ZN.2: 5 residues within 4Å: Chain A: H.85, H.87, H.154, C.173 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.85, A:H.87, A:H.154, H2O.4 ZN.3: 2 residues within 4Å: Chain A: E.117, D.188 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.117, A:E.117, A:D.188, H2O.4, H2O.4 ZN.7: 4 residues within 4Å: Chain B: D.89, C.173, K.176, H.215 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.89, B:C.173, B:H.215, H2O.6, H2O.7 ZN.8: 3 residues within 4Å: Chain B: H.85, H.87, H.154 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.85, B:H.87, B:H.154, H2O.7 ZN.9: 2 residues within 4Å: Chain B: E.117, D.188 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.117, B:D.188

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: D.60, D.95 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.60, A:D.95, H2O.2, H2O.3, H2O.5 CA.10: 2 residues within 4Å: Chain B: D.60, D.95 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.60, B:D.95, H2O.6, H2O.7

1 x N9M: benzyl (carboxyoxy)carbamate(Covalent)

N9M.5: 8 residues within 4Å: Chain A: F.35, V.38, K.176, A.180, S.182, G.184, H.215 Chain B: F.35 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.38, B:F.35 Hydrogen bonds: A:K.176 Water bridges: A:L.183, A:N.185 pi-Stacking: A:F.35

1 x N9J: benzyl hydroxycarbamate(Non-covalent)

N9J.6: 8 residues within 4Å: Chain A: P.33, G.34, F.35 Chain B: V.38, W.58, K.176, G.184, H.215 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B pi-Stacking: A:F.35 Hydrophobic interactions: B:V.38, B:V.38, B:W.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, P.W. et al., A Lysine-Targeted Affinity Label for Serine-beta-Lactamase Also Covalently Modifies New Delhi Metallo-beta-lactamase-1 (NDM-1). Biochemistry (2019)

Release Date

2019-06-12

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase