SMTL ID : 2bhb.1

Zn substituted E. coli Aminopeptidase P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-tetramer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.271, H.354, T.381, E.383, E.406 Ligands: ZN.2 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.9 ZN.2: 6 residues within 4Å: Chain A: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.260, A:D.260, A:D.271, A:E.406, H2O.9 ZN.5: 3 residues within 4Å: Chain A: D.48, R.166, H.170 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.48, A:H.170 ZN.6: 1 residues within 4Å: Chain A: H.71 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.71 ZN.8: 6 residues within 4Å: Chain B: D.271, H.354, T.381, E.383, E.406 Ligands: ZN.9 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.17 ZN.9: 6 residues within 4Å: Chain B: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.260, B:D.260, B:D.271, B:E.406, H2O.17 ZN.12: 3 residues within 4Å: Chain B: D.48, R.166, H.170 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.48, B:H.170 ZN.13: 1 residues within 4Å: Chain B: H.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.71 ZN.15: 6 residues within 4Å: Chain C: D.271, H.354, T.381, E.383, E.406 Ligands: ZN.16 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.25 ZN.16: 6 residues within 4Å: Chain C: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.260, C:D.260, C:D.271, C:E.406, H2O.25 ZN.19: 3 residues within 4Å: Chain C: D.48, R.166, H.170 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.48, C:H.170 ZN.20: 1 residues within 4Å: Chain C: H.71 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.71 ZN.22: 6 residues within 4Å: Chain D: D.271, H.354, T.381, E.383, E.406 Ligands: ZN.23 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.33 ZN.23: 6 residues within 4Å: Chain D: Y.229, D.260, D.271, T.273, E.406 Ligands: ZN.22 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.260, D:D.260, D:D.271, D:E.406, H2O.33 ZN.26: 3 residues within 4Å: Chain D: D.48, R.166, H.170 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.48, D:H.170 ZN.27: 1 residues within 4Å: Chain D: H.71 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.71

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: R.399 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain B: R.399 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain C: R.399 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain D: R.399 No protein-ligand interaction detected (PLIP)

4 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 4 residues within 4Å: Chain A: R.186, M.193, R.221, H.222 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.221, A:R.221 Salt bridges: A:R.186, A:R.186, A:H.222, A:H.222 FLC.11: 4 residues within 4Å: Chain B: R.186, M.193, R.221, H.222 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.221, B:R.221 Salt bridges: B:R.186, B:R.186, B:H.222, B:H.222 FLC.18: 4 residues within 4Å: Chain C: R.186, M.193, R.221, H.222 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.221, C:R.221 Salt bridges: C:R.186, C:R.186, C:H.222, C:H.222 FLC.25: 4 residues within 4Å: Chain D: R.186, M.193, R.221, H.222 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.221, D:R.221 Salt bridges: D:R.186, D:R.186, D:H.222, D:H.222

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.7: 6 residues within 4Å: Chain A: H.243, H.350, G.351, E.383, R.404 Chain B: W.88 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.88 Hydrogen bonds: A:H.243, A:H.350, A:G.351, A:G.351 Water bridges: A:R.370 MRD.14: 6 residues within 4Å: Chain A: W.88 Chain B: H.243, H.350, G.351, E.383, R.404 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.243, B:H.350, B:G.351 Water bridges: B:R.370 Hydrophobic interactions: A:W.88 MRD.21: 6 residues within 4Å: Chain C: H.243, H.350, G.351, E.383, R.404 Chain D: W.88 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.243, C:H.350, C:G.351 Water bridges: C:R.370 Hydrophobic interactions: D:W.88 MRD.28: 6 residues within 4Å: Chain C: W.88 Chain D: H.243, H.350, G.351, E.383, R.404 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.243, D:H.350, D:G.351, D:G.351 Water bridges: D:R.370 Hydrophobic interactions: C:W.88

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
A

B
A

C
A

D
A

XAA-PRO AMINOPEPTIDASE

Related Entries With Identical Sequence