SMTL ID : 3giu.1

1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.71, C.144, H.168 Chain B: T.214 Ligands: ACY.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.144, A:H.168, ACY.2 ZN.6: 5 residues within 4Å: Chain A: E.215 Chain B: Q.71, C.144, H.168 Ligands: ACY.7 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:Q.71, B:C.144, B:H.168, A:E.215, ACY.7

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 8 residues within 4Å: Chain A: F.11, F.14, N.20, T.45, G.70, Q.71, C.144 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.11, A:F.14, A:T.45 Hydrogen bonds: A:N.20, A:S.22, A:S.22, A:Q.71 ACY.7: 9 residues within 4Å: Chain A: E.215 Chain B: F.11, F.14, N.20, T.45, G.70, Q.71, C.144 Ligands: ZN.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.11, B:F.14, B:T.45 Hydrogen bonds: B:N.20, B:S.22, B:S.22, B:Q.71

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: N.76, A.77, I.127, G.130, L.131, P.132, G.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.76, A:G.133 PG4.4: 5 residues within 4Å: Chain A: I.87, D.102, Q.103, A.104 Chain B: F.114 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:F.114 Hydrogen bonds: A:A.104 PG4.9: 6 residues within 4Å: Chain B: N.76, I.127, G.130, L.131, P.132, G.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.133

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: D.97, F.98, Q.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.97, A:Q.99, A:Q.99 GOL.10: 5 residues within 4Å: Chain B: L.58, N.61, H.62, Y.63, Y.159 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.58, B:H.62, B:Y.63 Water bridges: B:Y.159, B:L.162

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 8 residues within 4Å: Chain B: S.115, N.116, L.117, P.118, V.119, R.163, D.204, D.206 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.204, B:D.206, B:D.206 Water bridges: B:R.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus. TO BE PUBLISHED

Release Date

2009-03-17

Peptides

Pyrrolidone-carboxylate peptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyrrolidone-carboxylate peptidase