SMTL ID : 8pbn.1

Mutant R1789Q of the dihydroorotase domain of human CAD protein bound to the inhibitor fluoorotate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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: 13 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: ZN.3 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.10: 13 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: ZN.12 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.2: 7 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.14, A:D.227, H2O.3 ZN.3: 7 residues within 4Å: Chain A: H.12, K.97, Y.99, H.131, H.155 Ligands: FOT.1, ZN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.3 ZN.11: 7 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: ZN.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.14, B:D.227, H2O.15 ZN.12: 7 residues within 4Å: Chain B: H.12, K.97, Y.99, H.131, H.155 Ligands: FOT.10, ZN.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.15

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

FMT.4: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.13 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.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:I.128, A:R.149 Water bridges: A:S.150, A:S.150 FMT.6: 5 residues within 4Å: Chain A: H.125, P.359, Q.360, L.361 Chain B: L.266 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.361 Water bridges: B:L.266, B:L.266 FMT.8: 7 residues within 4Å: Chain A: P.285, Q.286, E.287 Chain B: P.285, E.287, Q.355 Ligands: FMT.17 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:P.285, B:D.288, A:D.288 FMT.9: 4 residues within 4Å: Chain A: Q.330, Y.346, Q.348 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.348 FMT.13: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.4 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.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:I.128, B:R.149 Water bridges: B:S.150, B:S.150 FMT.15: 5 residues within 4Å: Chain A: L.266 Chain B: H.125, P.359, Q.360, L.361 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.361 Water bridges: A:L.266, A:L.266 FMT.17: 7 residues within 4Å: Chain A: P.285, E.287, Q.355 Chain B: P.285, Q.286, E.287 Ligands: FMT.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:P.285, A:D.288, B:D.288 FMT.18: 4 residues within 4Å: Chain B: Q.330, Y.346, Q.348 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.348

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: E.287, Q.330, Q.348, W.353, P.354, Q.355 Ligands: FMT.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.287, A:Q.355 Water bridges: A:Q.330, A:Q.348, A:Q.348 GOL.16: 7 residues within 4Å: Chain B: E.287, Q.330, Q.348, W.353, P.354, Q.355 Ligands: FMT.18 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.287, B:Q.355 Water bridges: B:Q.330, B:Q.348, B:Q.348

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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