SMTL ID : 4c6l.1

Crystal structure of the dihydroorotase domain of human CAD bound to the inhibitor fluoroorotate at pH 6.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.18, K.103, Y.105, H.137, H.161 Ligands: ZN.2, FOT.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.137, A:H.161, H2O.3 ZN.2: 7 residues within 4Å: Chain A: H.18, H.20, M.50, K.103, H.161, D.233 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, A:H.20, A:D.233, H2O.3 ZN.6: 7 residues within 4Å: Chain B: H.18, K.103, Y.105, H.137, H.161 Ligands: ZN.7, FOT.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.137, B:H.161, H2O.18 ZN.7: 7 residues within 4Å: Chain B: H.18, H.20, M.50, K.103, H.161, D.233 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.18, B:H.20, B:D.233, H2O.18

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

FMT.3: 7 residues within 4Å: Chain A: P.133, I.134, V.135, R.155, S.156, V.157, H.158 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.134, A:R.155, A:V.157 Water bridges: A:S.156, A:S.156, A:T.182 FMT.5: 3 residues within 4Å: Chain A: H.281, R.284, R.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.281, A:R.284 FMT.8: 7 residues within 4Å: Chain B: P.133, I.134, V.135, R.155, S.156, V.157, H.158 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.134, B:R.155, B:V.157 Water bridges: B:S.156, B:S.156, B:T.182 FMT.10: 3 residues within 4Å: Chain B: H.281, R.284, R.285 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.281, B:R.284

2 x FOT: 5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

FOT.4: 13 residues within 4Å: Chain A: H.20, R.22, N.52, K.103, Y.105, H.137, V.207, R.208, A.235, H.237, P.249, G.250 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.52, A:R.208, A:R.208, A:P.249, A:P.249 Salt bridges: A:H.20, A:R.22, A:H.237 Halogen bonds: A:N.52 FOT.9: 13 residues within 4Å: Chain B: H.20, R.22, N.52, K.103, Y.105, H.137, V.207, R.208, A.235, H.237, P.249, G.250 Ligands: ZN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.52, B:R.208, B:R.208, B:P.249, B:P.249 Salt bridges: B:H.20, B:R.22, B:H.237 Halogen bonds: B:N.52

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Grande-Garcia, A. et al., Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad. Structure (2014)

Release Date

2014-02-05

Peptides

CAD PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CAD PROTEIN

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