SMTL ID : 3wc5.1

Carboxypeptidase B in complex with DD9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: R.81, E.82, E.289 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.82, A:E.289, A:E.289, H2O.13 ZN.2: 6 residues within 4Å: Chain A: H.66, E.69, H.194, S.195 Ligands: DDK.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.66, A:E.69, A:E.69, A:H.194 ZN.4: 7 residues within 4Å: Chain A: E.69, S.195, Y.196, E.268 Ligands: ZN.2, DDK.3, CAC.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.195, A:E.268, A:E.268

1 x DDK: (2R)-7-amino-2-(selanylmethyl)heptanoic acid(Non-covalent)

DDK.3: 18 residues within 4Å: Chain A: H.66, E.69, R.124, N.141, R.142, H.194, S.195, L.201, S.205, I.245, Y.246, G.251, D.253, T.266, E.268 Ligands: ZN.2, ZN.4, CAC.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.201, A:I.245, A:Y.246 Hydrogen bonds: A:N.141, A:S.205, A:S.205, A:Y.246, A:Y.246 Water bridges: A:D.253 Salt bridges: A:H.66, A:R.124, A:R.142

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 8 residues within 4Å: Chain A: S.195, Y.196, I.245, Y.246, E.268, F.277 Ligands: DDK.3, ZN.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshimoto, N. et al., Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme. J.Med.Chem. (2013)

Release Date

2013-10-02

Peptides

Carboxypeptidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Carboxypeptidase B

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