SMTL ID : 1a16.1

AMINOPEPTIDASE P FROM E. COLI WITH THE INHIBITOR PRO-LEU

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x PRO: PROLINE(Non-covalent)

PRO.1: 8 residues within 4Å: Chain A: H.243, D.260, H.350, H.361, E.383, R.404 Chain D: W.88 Ligands: LEU.2 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: P.1, A:H.243 Hydrophobic interactions: A:H.350 PRO.5: 8 residues within 4Å: Chain B: H.243, D.260, H.350, H.361, E.383, R.404 Chain C: W.88 Ligands: LEU.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.350 Hydrogen bonds: B:H.243, P.5 PRO.9: 8 residues within 4Å: Chain B: W.88 Chain C: H.243, D.260, H.350, H.361, E.383, R.404 Ligands: LEU.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:H.350 Hydrogen bonds: C:H.243, P.9 PRO.13: 8 residues within 4Å: Chain A: W.88 Chain D: H.243, D.260, H.350, H.361, E.383, R.404 Ligands: LEU.14 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:H.350 Hydrogen bonds: D:H.243, P.13

4 x LEU: LEUCINE(Non-covalent)

LEU.2: 9 residues within 4Å: Chain A: H.350, G.351, H.354, H.361, Y.366, R.370 Chain B: R.153 Chain D: W.88 Ligands: PRO.1 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.351, A:G.351 Water bridges: A:G.351, B:R.153, L.2 Salt bridges: A:R.370, B:R.153 LEU.6: 9 residues within 4Å: Chain A: R.153 Chain B: H.350, G.351, H.354, H.361, Y.366, R.370 Chain C: W.88 Ligands: PRO.5 7 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B, 2 interactions with chain A Water bridges: L.6, B:G.351, A:R.153 Hydrogen bonds: B:G.351, B:G.351 Salt bridges: B:R.370, A:R.153 LEU.10: 9 residues within 4Å: Chain B: W.88 Chain C: H.350, G.351, H.354, H.361, Y.366, R.370 Chain D: R.153 Ligands: PRO.9 7 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 4 interactions with chain C Water bridges: D:R.153, L.10, C:G.351 Salt bridges: D:R.153, C:R.370 Hydrogen bonds: C:G.351, C:G.351 LEU.14: 9 residues within 4Å: Chain A: W.88 Chain C: R.153 Chain D: H.350, G.351, H.354, H.361, Y.366, R.370 Ligands: PRO.13 7 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain C, 4 interactions with chain D Water bridges: L.14, C:R.153, D:G.351 Salt bridges: C:R.153, D:R.370 Hydrogen bonds: D:G.351, D:G.351

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 6 residues within 4Å: Chain A: D.271, H.354, T.381, E.383, E.406 Ligands: MN.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.14 MN.4: 6 residues within 4Å: Chain A: Y.229, D.260, D.271, T.273, E.406 Ligands: MN.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.2, H2O.14 MN.7: 6 residues within 4Å: Chain B: D.271, H.354, T.381, E.383, E.406 Ligands: MN.8 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.27 MN.8: 6 residues within 4Å: Chain B: Y.229, D.260, D.271, T.273, E.406 Ligands: MN.7 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.27 MN.11: 6 residues within 4Å: Chain C: D.271, H.354, T.381, E.383, E.406 Ligands: MN.12 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.40 MN.12: 6 residues within 4Å: Chain C: Y.229, D.260, D.271, T.273, E.406 Ligands: MN.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.260, C:D.271, C:E.406, H2O.28, H2O.40 MN.15: 6 residues within 4Å: Chain D: D.271, H.354, T.381, E.383, E.406 Ligands: MN.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.54 MN.16: 6 residues within 4Å: Chain D: Y.229, D.260, D.271, T.273, E.406 Ligands: MN.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.42, H2O.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilce, M.C. et al., Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. Proc.Natl.Acad.Sci.USA (1998)

Release Date

1999-04-06

Peptides

AMINOPEPTIDASE P: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

AMINOPEPTIDASE P

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