SMTL ID : 1itu.1

HUMAN RENAL DIPEPTIDASE COMPLEXED WITH CILASTATIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: N.41, T.43, T.44, M.95, Y.96 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.96 Hydrogen bonds: A:N.41 NAG.2: 2 residues within 4Å: Chain A: N.316, T.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.316 NAG.6: 6 residues within 4Å: Chain B: E.38, N.41, T.43, T.44, M.95, Y.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.41, B:T.43 Water bridges: B:E.38 NAG.7: 2 residues within 4Å: Chain B: N.316, T.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.316, B:N.316

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: H.20, D.22, S.66, E.125, D.288 Ligands: ZN.4, CIL.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.20, A:D.22, A:D.22, A:E.125, H2O.1 ZN.4: 7 residues within 4Å: Chain A: H.20, E.125, H.198, H.219, R.230 Ligands: ZN.3, CIL.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.125, A:H.198, A:H.219, H2O.1 ZN.8: 8 residues within 4Å: Chain B: H.20, D.22, S.66, E.125, H.219, D.288 Ligands: ZN.9, CIL.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.20, B:D.22, B:E.125, H2O.14 ZN.9: 7 residues within 4Å: Chain B: H.20, E.125, H.198, H.219, R.230 Ligands: ZN.8, CIL.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.125, B:H.198, B:H.219, H2O.14

2 x CIL: CILASTATIN(Non-covalent)

CIL.5: 17 residues within 4Å: Chain A: D.22, W.25, Y.68, E.125, H.152, H.198, H.219, R.230, N.250, Y.252, Y.255, D.288, G.291, V.292, P.293 Ligands: ZN.3, ZN.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.68, A:Y.252, A:V.292 Hydrogen bonds: A:N.250, A:Y.255, A:G.291 Salt bridges: A:H.198, A:H.219, A:R.230 CIL.10: 16 residues within 4Å: Chain B: D.22, W.25, Y.68, E.125, H.152, H.198, H.219, R.230, Y.252, Y.255, D.288, G.291, V.292, P.293 Ligands: ZN.8, ZN.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.68, B:Y.252, B:V.292 Hydrogen bonds: B:N.250, B:Y.255, B:Y.255, B:G.291 Salt bridges: B:H.198, B:H.219, B:R.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nitanai, Y. et al., Crystal Structure of Human Renal Dipeptidase Involved in beta-Lactam Hydrolysis. J.Mol.Biol. (2002)

Release Date

2002-08-28

Peptides

RENAL DIPEPTIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RENAL DIPEPTIDASE

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