SMTL ID : 4pv4.1

Proline aminopeptidase P II from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: Y.227, D.258, D.269, T.271, E.405 Ligands: MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.258, A:D.258, A:D.269, A:E.405, H2O.19 MG.2: 6 residues within 4Å: Chain A: D.269, H.352, T.380, E.382, E.405 Ligands: MG.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.269, A:H.352, A:E.382, A:E.405, H2O.19 MG.6: 6 residues within 4Å: Chain B: D.269, H.352, T.380, E.382, E.405 Ligands: MG.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.269, B:H.352, B:E.382, B:E.405, H2O.33 MG.7: 7 residues within 4Å: Chain B: Y.227, D.258, D.269, T.271, E.405 Ligands: MG.6, P6G.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.258, B:D.258, B:D.269, B:E.405, H2O.33

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 11 residues within 4Å: Chain A: Y.227, I.230, L.240, H.241, D.258, H.348, H.352, H.359, E.382, R.403 Chain B: D.36 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.36

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: F.108, D.109, N.112, N.137, I.138, A.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.112

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: R.147, P.157, A.158, T.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.147, A:P.157 EDO.9: 4 residues within 4Å: Chain B: R.147, P.157, A.158, T.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.147, B:P.157 EDO.10: 5 residues within 4Å: Chain B: H.352, H.359, Y.364, R.369 Ligands: P6G.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.359

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.8: 13 residues within 4Å: Chain A: D.36, F.87 Chain B: Y.227, I.230, L.240, H.241, D.258, H.348, H.359, E.382, R.403 Ligands: MG.7, EDO.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Proline aminopeptidase P II from Yersinia pestis. To be Published

Release Date

2014-04-02

Peptides

Proline aminopeptidase P II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline aminopeptidase P II