SMTL ID : 2bww.1

His350Ala Escherichia coli Aminopeptidase P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.271, H.354, T.381, E.383, E.406 Ligands: MN.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.6 MN.2: 6 residues within 4Å: Chain A: Y.229, D.260, D.271, T.273, E.406 Ligands: MN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.260, A:D.271, A:E.406, H2O.6, H2O.6 MN.6: 6 residues within 4Å: Chain B: D.271, H.354, T.381, E.383, E.406 Ligands: MN.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.12 MN.7: 6 residues within 4Å: Chain B: Y.229, D.260, D.271, T.273, E.406 Ligands: MN.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.12, H2O.12 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.18 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.18, H2O.18 MN.16: 6 residues within 4Å: Chain D: D.271, H.354, T.381, E.383, E.406 Ligands: MN.17 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.24 MN.17: 6 residues within 4Å: Chain D: Y.229, D.260, D.271, T.273, E.406 Ligands: MN.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.260, D:D.271, D:E.406, H2O.24, H2O.24

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: R.399 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: R.399 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain C: R.399 No protein-ligand interaction detected (PLIP) MG.18: 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 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.9: 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.14: 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.19: 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

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

MRD.5: 8 residues within 4Å: Chain A: I.232, L.242, H.243, D.260, H.361, E.383, R.404 Chain B: W.88 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.232, B:W.88 Hydrogen bonds: A:L.242 Water bridges: A:D.260, A:D.260, A:D.260, A:E.383 MRD.10: 8 residues within 4Å: Chain A: W.88 Chain B: I.232, L.242, H.243, D.260, H.361, E.383, R.404 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.232, A:W.88 Hydrogen bonds: B:L.242 Water bridges: B:D.260, B:D.260, B:D.260, B:E.383 MRD.15: 8 residues within 4Å: Chain C: I.232, L.242, H.243, D.260, H.361, E.383, R.404 Chain D: W.88 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.232, D:W.88 Hydrogen bonds: C:L.242 Water bridges: C:D.260, C:D.260, C:D.260, C:E.383 MRD.20: 8 residues within 4Å: Chain C: W.88 Chain D: I.232, L.242, H.243, D.260, H.361, E.383, R.404 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:W.88, D:I.232 Hydrogen bonds: D:L.242 Water bridges: D:D.260, D:D.260, D:D.260, D:E.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graham, S.C. et al., Kinetic and Crystallographic Analysis of Mutant Escherichia Coli Aminopeptidase P: Insights Into Substrate Recognition and the Mechanism of Catalysis. Biochemistry (2006)

Release Date

2006-01-25

Peptides

AMINOPEPTIDASE P: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

AMINOPEPTIDASE P