SMTL ID : 3sfw.1

Crystal structure of dihydropyrimidinase from Brevibacillus agri NCHU1002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: A.243, R.247, V.299 Chain C: E.254 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.243, A:R.247, A:V.299 Salt bridges: A:R.247 Hydrogen bonds: C:E.254 ACT.3: 4 residues within 4Å: Chain A: G.47, Y.48, Y.49, P.398 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.49, A:P.398 Water bridges: A:T.9, A:G.47, A:G.47 ACT.5: 1 residues within 4Å: Chain A: K.277 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.285 Salt bridges: A:K.277 ACT.8: 4 residues within 4Å: Chain B: G.47, Y.48, Y.49, P.398 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.49, B:P.398 Hydrogen bonds: B:G.47 Water bridges: B:G.47 ACT.9: 5 residues within 4Å: Chain B: E.254, K.255 Chain D: A.243, R.247, V.299 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.299 Salt bridges: D:R.247 Hydrogen bonds: B:E.254 ACT.10: 1 residues within 4Å: Chain B: G.201 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.203 ACT.11: 4 residues within 4Å: Chain A: E.254 Chain C: A.243, R.247, V.299 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.243, C:R.247, C:V.299 Salt bridges: C:R.247 Hydrogen bonds: A:E.254 ACT.13: 4 residues within 4Å: Chain C: G.47, Y.48, Y.49, P.398 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.49, C:P.398 Water bridges: C:T.9, C:G.47, C:G.47 ACT.15: 1 residues within 4Å: Chain C: K.277 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.285 Salt bridges: C:K.277 ACT.18: 4 residues within 4Å: Chain D: G.47, Y.48, Y.49, P.398 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.49, D:P.398 Hydrogen bonds: D:G.47 Water bridges: D:G.47 ACT.19: 5 residues within 4Å: Chain B: A.243, R.247, V.299 Chain D: E.254, K.255 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.299 Salt bridges: B:R.247 Hydrogen bonds: D:E.254 ACT.20: 1 residues within 4Å: Chain D: G.201 1 PLIP interactions: 1 interactions with chain D Water bridges: D:T.203

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: K.150, H.183, H.239 Ligands: ZN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.183, A:H.239, H2O.11, H2O.16 ZN.4: 5 residues within 4Å: Chain A: H.58, H.60, K.150, D.315 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.58, A:H.60, A:D.315 ZN.6: 4 residues within 4Å: Chain B: K.150, H.183, H.239 Ligands: ZN.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.183, B:H.239, H2O.26, H2O.29 ZN.7: 5 residues within 4Å: Chain B: H.58, H.60, K.150, D.315 Ligands: ZN.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.58, B:H.60, B:D.315 ZN.12: 4 residues within 4Å: Chain C: K.150, H.183, H.239 Ligands: ZN.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.183, C:H.239, H2O.55, H2O.60 ZN.14: 5 residues within 4Å: Chain C: H.58, H.60, K.150, D.315 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.58, C:H.60, C:D.315 ZN.16: 4 residues within 4Å: Chain D: K.150, H.183, H.239 Ligands: ZN.17 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.183, D:H.239, H2O.70, H2O.73 ZN.17: 5 residues within 4Å: Chain D: H.58, H.60, K.150, D.315 Ligands: ZN.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.58, D:H.60, D:D.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W.C. et al., Crystal structure of dihydropyrimidinase from Brevibacillus agri NCHU1002. To be Published

Release Date

2012-06-20

Peptides

Dihydropyrimidinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydropyrimidinase