SMTL ID : 5k4m.1

Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.95, H.97, H.164 Ligands: SV7.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.95, A:H.97, A:H.164 ZN.2: 4 residues within 4Å: Chain A: D.99, C.183, H.225 Ligands: SV7.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.99, A:C.183, A:H.225

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 4 residues within 4Å: Chain A: R.60, N.151, F.152, G.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.60, A:N.151, A:G.153 Water bridges: A:F.152

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: E.127, E.198 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.127, A:E.127, A:E.198, H2O.1 MG.5: 1 residues within 4Å: Chain A: D.70 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.70, H2O.3, H2O.3, H2O.5, H2O.7

2 x SV7: phenylphosphonic acid(Non-covalent)

SV7.6: 2 residues within 4Å: Chain A: V.25, Y.39 No protein-ligand interaction detected (PLIP) SV7.8: 10 residues within 4Å: Chain A: M.42, V.48, H.95, H.97, D.99, H.164, C.183, H.225 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.48 Water bridges: A:N.195, A:N.195, A:N.195

1 x NPO: P-NITROPHENOL(Non-covalent)

NPO.7: 2 residues within 4Å: Chain A: A.71, A.74 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baier, F. et al., Enzyme evolvability is contingent on the initial sequence background. To Be Published

Release Date

2017-04-26

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

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