SMTL ID : 4tqt.1 (1 other biounit)

Crystal structure of Dihydropyrimidinase from Brucella suis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.69, H.71, K.159, D.325 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.69, A:H.71, A:D.325 ZN.2: 5 residues within 4Å: Chain A: K.159, H.192, H.248, S.298 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.192, A:H.248 ZN.8: 5 residues within 4Å: Chain B: H.69, H.71, K.159, D.325 Ligands: ZN.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.69, B:H.71, B:D.325 ZN.9: 4 residues within 4Å: Chain B: K.159, H.192, H.248 Ligands: ZN.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.192, B:H.248, H2O.9 ZN.13: 5 residues within 4Å: Chain C: H.69, H.71, K.159, D.325 Ligands: ZN.14 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.69, C:H.71, C:D.325 ZN.14: 4 residues within 4Å: Chain C: K.159, H.192, H.248 Ligands: ZN.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.192, C:H.248 ZN.19: 5 residues within 4Å: Chain D: H.69, H.71, K.159, D.325 Ligands: ZN.20 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.69, D:H.71, D:D.325 ZN.20: 4 residues within 4Å: Chain D: K.159, H.192, H.248 Ligands: ZN.19 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.192, D:H.248

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

EDO.3: 7 residues within 4Å: Chain A: D.308, W.311, R.367 Chain B: K.264, G.265, W.477 Ligands: EDO.7 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Q.320, N.380, K.383 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: N.156, G.186, I.384, N.386, N.467, G.468, N.471 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: G.265, R.267, L.474, W.477 Chain B: G.366, R.367 Ligands: EDO.10 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: A.315, G.366, R.367 Chain B: G.265, R.267, W.477 Ligands: EDO.3 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: K.264, G.265, W.477 Chain B: D.308, W.311, R.367 Ligands: EDO.6 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: Q.320, N.380, K.383, I.384 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: N.156, G.186, I.384, N.386, N.467, G.468, N.471 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain C: D.308, W.311, R.367 Chain D: K.264, W.477 Ligands: EDO.24 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: Q.320, N.380, K.383 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain C: N.156, G.186, I.384, N.386, P.466, N.467, G.468, N.471 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: G.265, R.267, L.474, W.477 Chain D: G.366, R.367 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain C: K.264, G.265, W.477 Chain D: D.308, W.311, A.312, R.367 Ligands: EDO.18 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: Q.320, N.380, K.383 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain D: N.156, G.186, I.384, N.386, N.467, G.468, N.471 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: G.366, R.367 Chain D: G.265, R.267, L.474, W.477 Ligands: EDO.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal structure of Dihydropyrimidinase from Brucella suis. to be published

Release Date

2014-08-06

Peptides

D-hydantoinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-hydantoinase

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