SMTL ID : 8pbs.1

Mutant K1482M of the dihydroorotase domain of human CAD protein in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.69, F.307, G.338, Q.339, V.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.69 GOL.11: 5 residues within 4Å: Chain B: R.69, F.307, G.338, Q.339, V.340 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.69

12 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.2 ZN.3: 5 residues within 4Å: Chain A: H.12, K.97, H.131, H.155 Ligands: ZN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.2 ZN.4: 3 residues within 4Å: Chain A: H.282 Chain B: H.275 Ligands: FMT.10 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.282, B:H.275, H2O.5 ZN.5: 2 residues within 4Å: Chain A: H.231, E.235 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.231, A:E.235, A:E.235, H2O.2 ZN.6: 4 residues within 4Å: Chain A: E.65, G.345, G.347, Q.348 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.65, A:G.345, A:G.347 ZN.7: 2 residues within 4Å: Chain A: D.294, H.297 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.294, A:H.297 ZN.12: 7 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, 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.4 ZN.13: 5 residues within 4Å: Chain B: H.12, K.97, H.131, H.155 Ligands: ZN.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.4 ZN.14: 3 residues within 4Å: Chain A: H.275 Chain B: H.282 Ligands: FMT.20 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.282, A:H.275, H2O.2 ZN.15: 2 residues within 4Å: Chain B: H.231, E.235 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.231, B:E.235, B:E.235, H2O.4 ZN.16: 4 residues within 4Å: Chain B: E.65, G.345, G.347, Q.348 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.65, B:G.345, B:G.347 ZN.17: 2 residues within 4Å: Chain B: D.294, H.297 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.294, B:H.297

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

FMT.8: 8 residues within 4Å: Chain A: L.126, P.127, I.128, R.149, S.150, V.151, H.152, I.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.128, A:R.149, A:S.150 FMT.9: 6 residues within 4Å: Chain A: H.275, R.278 Chain B: H.275, R.278, R.279 Ligands: FMT.19 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.275, A:R.278, A:R.278, B:H.275, B:R.278, B:R.278 FMT.10: 10 residues within 4Å: Chain A: H.282, L.283, P.284, Q.355, G.356, A.357, V.358, P.359 Chain B: H.275 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.282 Water bridges: A:A.357 FMT.18: 8 residues within 4Å: Chain B: L.126, P.127, I.128, R.149, S.150, V.151, H.152, I.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.128, B:R.149, B:S.150 FMT.19: 6 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278 Ligands: FMT.9 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.275, A:R.278, A:R.278, B:H.275, B:R.278, B:R.278 FMT.20: 10 residues within 4Å: Chain A: H.275 Chain B: H.282, L.283, P.284, Q.355, G.356, A.357, V.358, P.359 Ligands: ZN.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.282 Water bridges: B:A.357

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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