SMTL ID : 2bha.1

E. coli Aminopeptidase P in complex with substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x VAL- PRO- LEU: VALINE-PROLINE-LEUCINE(Non-covalent)

VAL-PRO-LEU.1: 16 residues within 4Å: Chain A: Y.229, H.243, D.260, D.271, H.350, G.351, H.354, V.360, H.361, Y.366, R.370, E.383, R.404, E.406 Chain B: W.88 Chain C: R.153 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain A Salt bridges: C:R.153, A:R.370 Hydrophobic interactions: A:Y.229, A:H.350, A:V.360 Hydrogen bonds: A:D.260, A:G.351, A:G.351 Water bridges: A:E.383, A:E.383 VAL-PRO-LEU.4: 16 residues within 4Å: Chain A: W.88 Chain B: Y.229, H.243, D.260, D.271, H.350, G.351, H.354, V.360, H.361, Y.366, R.370, E.383, R.404, E.406 Chain D: R.153 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.229, B:H.350, B:V.360 Hydrogen bonds: B:D.260, B:G.351 Water bridges: B:E.383, B:E.383 Salt bridges: B:R.370, D:R.153 VAL-PRO-LEU.7: 16 residues within 4Å: Chain A: R.153 Chain C: Y.229, H.243, D.260, D.271, H.350, G.351, H.354, V.360, H.361, Y.366, R.370, E.383, R.404, E.406 Chain D: W.88 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.229, C:H.350, C:V.360 Hydrogen bonds: C:D.260, C:G.351 Water bridges: C:E.383, C:E.383 Salt bridges: C:R.370, A:R.153 VAL-PRO-LEU.10: 16 residues within 4Å: Chain B: R.153 Chain C: W.88 Chain D: Y.229, H.243, D.260, D.271, H.350, G.351, H.354, V.360, H.361, Y.366, R.370, E.383, R.404, E.406 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.229, D:H.350, D:V.360 Hydrogen bonds: D:D.260, D:G.351, D:G.351 Water bridges: D:E.383, D:E.383 Salt bridges: D:R.370, B:R.153

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: R.399 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: R.399 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain C: R.399 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain D: R.399 No protein-ligand interaction detected (PLIP)

4 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 4 residues within 4Å: Chain A: R.186, M.193, R.221, H.222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.221 Salt bridges: A:R.186, A:R.186, A:H.222, A:H.222 FLC.6: 4 residues within 4Å: Chain B: R.186, M.193, R.221, H.222 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.221 Salt bridges: B:R.186, B:R.186, B:H.222, B:H.222 FLC.9: 4 residues within 4Å: Chain C: R.186, M.193, R.221, H.222 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.221 Salt bridges: C:R.186, C:R.186, C:H.222, C:H.222 FLC.12: 4 residues within 4Å: Chain D: R.186, M.193, R.221, H.222 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.221 Salt bridges: D:R.186, D:R.186, D:H.222, D:H.222

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

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