SMTL ID : 1wy2.1

Crystal Structure of the Prolidase from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.1: 12 residues within 4Å: Chain A: F.181, I.184, H.195, D.212, D.223, H.287, V.293, H.294, E.316, E.330 Ligands: ZN.2, ZN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.195 CAC.7: 11 residues within 4Å: Chain B: F.181, I.184, D.212, D.223, H.287, V.293, H.294, E.316, E.330 Ligands: ZN.8, ZN.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.212

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: F.181, D.212, D.223, T.225, E.316, E.330 Ligands: CAC.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.212, A:D.212, A:D.223, A:E.330 ZN.3: 7 residues within 4Å: Chain A: D.223, H.287, T.314, E.316, E.330 Ligands: CAC.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.223, A:H.287, A:E.316, A:E.330 ZN.8: 8 residues within 4Å: Chain B: F.181, D.212, D.223, T.225, E.316, E.330 Ligands: CAC.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.212, B:D.212, B:D.223, B:E.330 ZN.9: 7 residues within 4Å: Chain B: D.223, H.287, T.314, E.316, E.330 Ligands: CAC.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.223, B:H.287, B:E.316, B:E.330

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: T.53 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: K.27, N.30, E.94, S.95, S.96, D.118, R.125, W.296 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.30, A:S.95, A:R.125 Water bridges: A:I.93, A:V.117 GOL.6: 6 residues within 4Å: Chain A: K.27, R.125, E.292, E.295, W.296 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.27, A:R.125, A:E.292 Water bridges: A:W.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizutani, H. et al., Crystal Structure of the Prolidase from Pyrococcus horikoshii OT3. To be Published

Release Date

2005-02-22

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase