SMTL ID : 8pbm.1

Mutant R1789Q of the dihydroorotase domain of human CAD protein bound to the substrate dihydroorotate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-dimer

Ligands

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

DOR.1: 17 residues within 4Å: Chain A: H.14, R.16, N.46, K.97, Y.99, T.103, F.104, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.7, ZN.8 8 PLIP interactions: 8 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 DOR.11: 17 residues within 4Å: Chain B: H.14, R.16, N.46, K.97, Y.99, T.103, F.104, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.17, ZN.18 8 PLIP interactions: 8 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.287, Q.330, Q.348, W.353, Q.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.355 Water bridges: A:Q.330, A:Q.348 GOL.4: 5 residues within 4Å: Chain A: E.332, L.341, V.342, P.343, Y.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.332, A:L.341 Water bridges: A:V.333 GOL.12: 5 residues within 4Å: Chain B: E.287, Q.330, Q.348, W.353, Q.355 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.355 Water bridges: B:Q.330, B:Q.348 GOL.14: 5 residues within 4Å: Chain B: E.332, L.341, V.342, P.343, Y.346 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.332, B:E.332, B:L.341 Water bridges: B:V.333

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

FMT.3: 8 residues within 4Å: Chain A: L.126, P.127, I.128, V.129, R.149, S.150, V.151, H.152 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.128, A:R.149, A:S.150 Water bridges: A:S.150, A:S.150, A:T.176 FMT.5: 6 residues within 4Å: Chain A: E.65, A.66, G.345, Y.346, Q.348 Ligands: ZN.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.65, A:G.345 FMT.6: 3 residues within 4Å: Chain A: H.297, W.299, T.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.297 FMT.13: 8 residues within 4Å: Chain B: L.126, P.127, I.128, V.129, R.149, S.150, V.151, H.152 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.128, B:R.149, B:S.150 Water bridges: B:S.150, B:S.150, B:T.176 FMT.15: 6 residues within 4Å: Chain B: E.65, A.66, G.345, Y.346, Q.348 Ligands: ZN.19 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.65, B:G.345 FMT.16: 3 residues within 4Å: Chain B: H.297, W.299, T.323 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.297

8 x ZN: ZINC ION(Non-covalent)

ZN.7: 8 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: DOR.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.1 ZN.8: 7 residues within 4Å: Chain A: H.12, K.97, Y.99, H.131, H.155 Ligands: DOR.1, ZN.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.1 ZN.9: 5 residues within 4Å: Chain A: E.65, G.345, G.347, Q.348 Ligands: FMT.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, A:G.345, A:G.347, H2O.12 ZN.10: 2 residues within 4Å: Chain A: H.275 Chain B: H.282 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.275, H2O.12 ZN.17: 8 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: DOR.11, ZN.18 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 ZN.18: 7 residues within 4Å: Chain B: H.12, K.97, Y.99, H.131, H.155 Ligands: DOR.11, ZN.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.16 ZN.19: 5 residues within 4Å: Chain B: E.65, G.345, G.347, Q.348 Ligands: FMT.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.65, B:G.345, B:G.347, H2O.27 ZN.20: 2 residues within 4Å: Chain A: H.282 Chain B: H.275 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.275, H2O.27

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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