SMTL ID : 8pbk.1

Mutant R1722W of the dihydroorotase domain of human CAD protein bound to the inhibitor fluoorotate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

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

FOT.1: 14 residues within 4Å: Chain A: H.14, R.16, N.46, K.97, Y.99, H.131, V.201, R.202, A.229, H.231, P.243, G.244 Ligands: FMT.3, ZN.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.46, A:N.46, A:R.202, A:R.202, A:P.243 Salt bridges: A:H.14, A:R.16, A:H.231 Halogen bonds: A:N.46 FOT.8: 14 residues within 4Å: Chain B: H.14, R.16, N.46, K.97, Y.99, H.131, V.201, R.202, A.229, H.231, P.243, G.244 Ligands: FMT.10, ZN.13 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.46, B:N.46, B:R.202, B:R.202, B:P.243 Salt bridges: B:H.14, B:R.16, B:H.231 Halogen bonds: B:N.46

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: V.211, E.212, W.215, W.263 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.215 GOL.9: 4 residues within 4Å: Chain B: V.211, E.212, W.215, W.263 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.215

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

FMT.3: 5 residues within 4Å: Chain A: N.46, T.103, F.104, P.243 Ligands: FOT.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.46, A:N.46, A:T.103 FMT.4: 8 residues within 4Å: Chain A: P.127, I.128, V.129, R.149, S.150, V.151, H.152 Ligands: FMT.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.128, A:R.149, A:S.150 Water bridges: A:S.150, A:S.150 FMT.5: 7 residues within 4Å: Chain A: S.124, H.125, L.126, R.149, S.150 Chain B: D.267 Ligands: FMT.4 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:D.267, B:D.267, A:S.150 Hydrogen bonds: A:R.149, A:S.150 FMT.10: 5 residues within 4Å: Chain B: N.46, T.103, F.104, P.243 Ligands: FOT.8 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.46, B:N.46, B:T.103 FMT.11: 8 residues within 4Å: Chain B: P.127, I.128, V.129, R.149, S.150, V.151, H.152 Ligands: FMT.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.128, B:R.149, B:S.150 Water bridges: B:S.150, B:S.150 FMT.12: 7 residues within 4Å: Chain A: D.267 Chain B: S.124, H.125, L.126, R.149, S.150 Ligands: FMT.11 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:D.267, B:S.150 Hydrogen bonds: B:R.149, B:S.150

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 7 residues within 4Å: Chain A: H.12, K.97, Y.99, H.131, H.155 Ligands: FOT.1, ZN.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.2 ZN.7: 8 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.14, A:D.227, H2O.2 ZN.13: 7 residues within 4Å: Chain B: H.12, K.97, Y.99, H.131, H.155 Ligands: FOT.8, ZN.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.16 ZN.14: 8 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: ZN.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.14, B:D.227, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Del Cano-Ochoa, F. et al., Beyond genetics: Deciphering the impact of missense variants in CAD deficiency. J Inherit Metab Dis (2023)

Release Date

2023-11-01

Peptides

CAD protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CAD protein

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