SMTL ID : 6hg3.1

Hybrid dihydroorotase domain of human CAD with E. coli flexible loop, bound to dihydroorotate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: H.283, R.286, R.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.283, A:R.286 FMT.2: 6 residues within 4Å: Chain A: P.135, I.136, R.157, S.158, V.159, H.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.136, A:I.136, A:R.157 Water bridges: A:S.158, A:S.158 FMT.5: 4 residues within 4Å: Chain A: S.132, H.133, R.157, S.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.132, A:S.158 Water bridges: A:R.157, A:R.157 FMT.7: 3 residues within 4Å: Chain B: H.283, R.286, R.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.283, B:R.286 FMT.8: 6 residues within 4Å: Chain B: P.135, I.136, R.157, S.158, V.159, H.160 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.136, B:I.136, B:R.157 Water bridges: B:S.158, B:S.158 FMT.11: 4 residues within 4Å: Chain B: S.132, H.133, R.157, S.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.132, B:S.158 Water bridges: B:R.157, B:R.157

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: H.18, K.103, Y.105, H.139, H.163 Ligands: ZN.4, DOR.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.139, A:H.163, H2O.6 ZN.4: 8 residues within 4Å: Chain A: H.18, H.20, M.50, K.103, H.163, D.235 Ligands: ZN.3, DOR.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.18, A:H.20, A:D.235, H2O.1, H2O.6 ZN.9: 7 residues within 4Å: Chain B: H.18, K.103, Y.105, H.139, H.163 Ligands: ZN.10, DOR.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.139, B:H.163, H2O.17 ZN.10: 8 residues within 4Å: Chain B: H.18, H.20, M.50, K.103, H.163, D.235 Ligands: ZN.9, DOR.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.18, B:H.20, B:D.235, H2O.12, H2O.17

2 x DOR: (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

DOR.6: 14 residues within 4Å: Chain A: H.20, R.22, N.52, Y.105, H.139, V.209, R.210, D.235, A.237, H.239, P.251, G.252 Ligands: ZN.3, ZN.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.52, A:Y.105, A:R.210, A:R.210, A:P.251 Water bridges: A:H.239, A:F.253 Salt bridges: A:H.20, A:R.22, A:H.239 DOR.12: 14 residues within 4Å: Chain B: H.20, R.22, N.52, Y.105, H.139, V.209, R.210, D.235, A.237, H.239, P.251, G.252 Ligands: ZN.9, ZN.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.52, B:Y.105, B:R.210, B:R.210, B:P.251 Water bridges: B:H.239, B:F.253 Salt bridges: B:H.20, B:R.22, B:H.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Del Cano-Ochoa, F. et al., Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD. J. Biol. Chem. (2018)

Release Date

2018-10-24

Peptides

CAD protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CAD protein