SMTL ID : 8pbg.1

Mutant K1556T of the dihydroorotase domain of human CAD protein bound to the inhibitor fluoroorotate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

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

FMT.1: 10 residues within 4Å: Chain A: H.12, H.14, M.44, T.97, Y.99, H.131, H.155 Ligands: FOT.2, ZN.7, ZN.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.99, A:Y.99 FMT.3: 4 residues within 4Å: Chain A: A.31, R.69, F.307, V.340 No protein-ligand interaction detected (PLIP) FMT.4: 3 residues within 4Å: Chain A: M.142, Q.145, L.173 No protein-ligand interaction detected (PLIP) FMT.5: 8 residues within 4Å: Chain A: P.127, I.128, V.129, R.149, S.150, V.151, H.152, I.280 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.128, A:R.149, A:S.150, A:S.150 Water bridges: A:T.176 FMT.6: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.15 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.275, A:R.278, B:H.275, B:R.278 FMT.10: 10 residues within 4Å: Chain B: H.12, H.14, M.44, T.97, Y.99, H.131, H.155 Ligands: FOT.11, ZN.16, ZN.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.99, B:Y.99 FMT.12: 4 residues within 4Å: Chain B: A.31, R.69, F.307, V.340 No protein-ligand interaction detected (PLIP) FMT.13: 3 residues within 4Å: Chain B: M.142, Q.145, L.173 No protein-ligand interaction detected (PLIP) FMT.14: 8 residues within 4Å: Chain B: P.127, I.128, V.129, R.149, S.150, V.151, H.152, I.280 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.128, B:R.149, B:S.150, B:S.150 Water bridges: B:T.176 FMT.15: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.275, A:R.278, B:H.275, B:R.278

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

FOT.2: 14 residues within 4Å: Chain A: H.14, R.16, N.46, Y.99, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: FMT.1, ZN.8 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.11: 14 residues within 4Å: Chain B: H.14, R.16, N.46, Y.99, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: FMT.10, ZN.17 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

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 7 residues within 4Å: Chain A: H.12, H.14, M.44, H.155, D.227 Ligands: FMT.1, ZN.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.14, A:D.227, H2O.4 ZN.8: 7 residues within 4Å: Chain A: H.12, Y.99, H.131, H.155 Ligands: FMT.1, FOT.2, ZN.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.4 ZN.16: 7 residues within 4Å: Chain B: H.12, H.14, M.44, H.155, D.227 Ligands: FMT.10, ZN.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.14, B:D.227, H2O.19 ZN.17: 7 residues within 4Å: Chain B: H.12, Y.99, H.131, H.155 Ligands: FMT.10, FOT.11, ZN.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.19

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: E.65, G.345, G.347, Q.348 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.65 NA.18: 4 residues within 4Å: Chain B: E.65, G.345, G.347, Q.348 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.347

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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