SMTL ID : 2v3z.1

Glu383Ala Escherichia coli aminopeptidase P in complex with substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-tetramer

Ligands

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

VAL-PRO-LEU.1: 17 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, R.404, E.406 Chain B: R.153 Chain D: W.88 Ligands: MN.2, MN.3 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.229, A:H.350, A:H.354, A:V.360 Hydrogen bonds: A:D.260, A:G.351 Water bridges: A:G.351, B:R.153, B:R.153 Salt bridges: B:R.153 VAL-PRO-LEU.5: 17 residues within 4Å: Chain A: R.153 Chain B: Y.229, H.243, D.260, D.271, H.350, G.351, H.354, V.360, H.361, Y.366, R.370, R.404, E.406 Chain C: W.88 Ligands: MN.6, MN.7 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.229, B:H.350, B:H.354, B:V.360 Hydrogen bonds: B:D.260, B:G.351 Water bridges: B:G.351, A:R.153, A:R.153 Salt bridges: A:R.153 VAL-PRO-LEU.9: 17 residues within 4Å: Chain B: W.88 Chain C: Y.229, H.243, D.260, D.271, H.350, G.351, H.354, V.360, H.361, Y.366, R.370, R.404, E.406 Chain D: R.153 Ligands: MN.10, MN.11 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.229, C:H.350, C:H.354, C:V.360 Hydrogen bonds: C:G.351, C:H.354 Water bridges: C:G.351, C:G.351, D:R.153, D:R.153 Salt bridges: D:R.153 VAL-PRO-LEU.13: 17 residues within 4Å: Chain A: W.88 Chain C: R.153 Chain D: Y.229, H.243, D.260, D.271, H.350, G.351, H.354, V.360, H.361, Y.366, R.370, R.404, E.406 Ligands: MN.14, MN.15 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.229, D:H.350, D:H.354, D:V.360 Hydrogen bonds: D:G.351, D:H.354 Water bridges: D:G.351, D:G.351, C:R.153, C:R.153 Salt bridges: C:R.153

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

MN.2: 6 residues within 4Å: Chain A: D.271, H.354, T.381, E.406 Ligands: VAL-PRO-LEU.1, MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.271, A:H.354, A:E.406, H2O.27 MN.3: 7 residues within 4Å: Chain A: Y.229, D.260, D.271, T.273, E.406 Ligands: VAL-PRO-LEU.1, MN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.260, A:D.260, A:D.271, A:E.406 MN.6: 6 residues within 4Å: Chain B: D.271, H.354, T.381, E.406 Ligands: VAL-PRO-LEU.5, MN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.271, B:H.354, B:E.406, H2O.55 MN.7: 7 residues within 4Å: Chain B: Y.229, D.260, D.271, T.273, E.406 Ligands: VAL-PRO-LEU.5, MN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.260, B:D.260, B:D.271, B:E.406 MN.10: 6 residues within 4Å: Chain C: D.271, H.354, T.381, E.406 Ligands: VAL-PRO-LEU.9, MN.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.271, C:H.354, C:E.406, H2O.83 MN.11: 7 residues within 4Å: Chain C: Y.229, D.260, D.271, T.273, E.406 Ligands: VAL-PRO-LEU.9, MN.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.260, C:D.260, C:D.271, C:E.406 MN.14: 6 residues within 4Å: Chain D: D.271, H.354, T.381, E.406 Ligands: VAL-PRO-LEU.13, MN.15 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.271, D:H.354, D:E.406, H2O.111 MN.15: 7 residues within 4Å: Chain D: Y.229, D.260, D.271, T.273, E.406 Ligands: VAL-PRO-LEU.13, MN.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.260, D:D.260, D:D.271, D:E.406

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

CL.4: 4 residues within 4Å: Chain A: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.16: 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., Complexes of Mutants of Escherichia Coli Aminopeptidase P and the Tripeptide Substrate Valproleu. Arch.Biochem.Biophys. (2008)

Release Date

2007-11-20

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