SMTL ID : 8pbr.1

Mutant R1475Q of the dihydroorotase domain of human CAD protein in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.13, H.15, M.45, K.98, H.156, D.228 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.13, A:H.15, A:D.228, H2O.1 ZN.2: 5 residues within 4Å: Chain A: H.13, K.98, H.132, H.156 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.132, A:H.156, H2O.1 ZN.3: 4 residues within 4Å: Chain A: E.66, G.346, G.348, Q.349 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.66, A:G.346, A:G.348, H2O.5, H2O.6 ZN.8: 7 residues within 4Å: Chain B: H.13, H.15, M.45, K.98, H.156, D.228 Ligands: ZN.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.13, B:H.15, B:D.228, H2O.8 ZN.9: 5 residues within 4Å: Chain B: H.13, K.98, H.132, H.156 Ligands: ZN.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.132, B:H.156, H2O.8 ZN.10: 4 residues within 4Å: Chain B: E.66, G.346, G.348, Q.349 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.66, B:G.346, B:G.348, H2O.11, H2O.12

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

FMT.4: 9 residues within 4Å: Chain A: L.127, P.128, I.129, R.150, S.151, V.152, H.153, I.281 Ligands: FMT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.129, A:R.150, A:S.151 FMT.5: 7 residues within 4Å: Chain A: H.276, R.279, R.280 Chain B: H.276, R.279, R.280 Ligands: FMT.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.276, B:R.279, A:H.276, A:R.279 FMT.6: 3 residues within 4Å: Chain A: P.344, G.346, Y.347 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.347 FMT.7: 8 residues within 4Å: Chain A: H.126, L.127, P.128, R.150, S.151, I.281, H.283 Ligands: FMT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.151, A:H.283 FMT.11: 9 residues within 4Å: Chain B: L.127, P.128, I.129, R.150, S.151, V.152, H.153, I.281 Ligands: FMT.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.129, B:R.150, B:S.151 FMT.12: 7 residues within 4Å: Chain A: H.276, R.279, R.280 Chain B: H.276, R.279, R.280 Ligands: FMT.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.276, B:R.279, A:H.276, A:R.279 FMT.13: 3 residues within 4Å: Chain B: P.344, G.346, Y.347 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.347 FMT.14: 8 residues within 4Å: Chain B: H.126, L.127, P.128, R.150, S.151, I.281, H.283 Ligands: FMT.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.151, B:H.283

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