SMTL ID : 1w7v.2 (1 other biounit)

ZnMg substituted aminopeptidase P from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x PRO- LEU: PEPTIDE VAL-PRO-LEU(Non-covalent)

PRO-LEU.1: 12 residues within 4Å: Chain A: H.243, D.260, H.350, G.351, H.354, H.361, Y.366, R.370, E.383, R.404 Chain B: R.153 Chain C: W.88 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.243, A:G.351 Salt bridges: A:R.370, B:R.153 PRO-LEU.2: 12 residues within 4Å: Chain A: R.153 Chain B: H.243, D.260, H.350, G.351, H.354, H.361, Y.366, R.370, E.383, R.404 Chain D: W.88 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.243, B:G.351 Water bridges: B:E.383, B:E.383 Salt bridges: B:R.370, A:R.153 PRO-LEU.10: 12 residues within 4Å: Chain A: W.88 Chain C: H.243, D.260, H.350, G.351, H.354, H.361, Y.366, R.370, E.383, R.404 Chain D: R.153 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:R.153, C:R.370 Hydrogen bonds: C:G.351, C:E.383 PRO-LEU.11: 12 residues within 4Å: Chain B: W.88 Chain C: R.153 Chain D: H.243, D.260, H.350, G.351, H.354, H.361, Y.366, R.370, E.383, R.404 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.351, D:E.383 Water bridges: D:G.351, D:E.383 Salt bridges: D:R.370, C:R.153

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.271, H.354, T.381, E.383, E.406 Ligands: MG.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.271, A:H.354, A:E.383, A:E.406, H2O.6 ZN.6: 6 residues within 4Å: Chain B: D.271, H.354, T.381, E.383, E.406 Ligands: MG.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.271, B:H.354, B:E.383, B:E.406, H2O.19 ZN.12: 6 residues within 4Å: Chain C: D.271, H.354, T.381, E.383, E.406 Ligands: MG.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.271, C:H.354, C:E.383, C:E.406, H2O.24 ZN.15: 6 residues within 4Å: Chain D: D.271, H.354, T.381, E.383, E.406 Ligands: MG.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.271, D:H.354, D:E.383, D:E.406, H2O.37

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.260, A:D.271, A:E.406, H2O.5, H2O.6 MG.7: 6 residues within 4Å: Chain B: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.260, B:D.271, B:E.406, H2O.15, H2O.19 MG.8: 1 residues within 4Å: Chain B: R.399 No protein-ligand interaction detected (PLIP) MG.13: 6 residues within 4Å: Chain C: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.12 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.260, C:D.271, C:E.406, H2O.23, H2O.24 MG.16: 6 residues within 4Å: Chain D: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.260, D:D.271, D:E.406, H2O.33, H2O.37 MG.17: 1 residues within 4Å: Chain D: R.399 No protein-ligand interaction detected (PLIP)

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain D: R.79, V.80, F.110, S.111 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graham, S.C. et al., Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, a Metalloprotease with a Dinuclear Metal Center. Biochemistry (2005)

Release Date

2005-09-29

Peptides

XAA-PRO AMINOPEPTIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

XAA-PRO AMINOPEPTIDASE

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