SMTL ID : 8pbq.1

Mutant R1810Q of the dihydroorotase domain of human CAD protein bound to the substrates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

2 x NCD: N-CARBAMOYL-L-ASPARTATE(Non-covalent)

NCD.1: 19 residues within 4Å: Chain A: H.12, H.14, R.16, N.46, K.97, Y.99, T.103, F.104, H.131, H.155, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.3, ZN.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.46, A:T.103, A:R.202, A:R.202, A:P.243 Salt bridges: A:H.12, A:H.14, A:H.14, A:R.16, A:H.131, A:H.155, A:H.231 NCD.8: 19 residues within 4Å: Chain B: H.12, H.14, R.16, N.46, K.97, Y.99, T.103, F.104, H.131, H.155, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.10, ZN.11 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.46, B:T.103, B:R.202, B:R.202, B:P.243 Salt bridges: B:H.12, B:H.14, B:H.14, B:R.16, B:H.131, B:H.155, B:H.231

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

FMT.2: 9 residues within 4Å: Chain A: L.126, P.127, I.128, V.129, 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: 9 residues within 4Å: Chain B: L.126, P.127, I.128, V.129, 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

10 x ZN: ZINC ION(Non-covalent)

ZN.3: 8 residues within 4Å: Chain A: H.12, K.97, Y.99, T.103, H.131, H.155 Ligands: NCD.1, ZN.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.131, A:H.155 ZN.4: 9 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: NCD.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.12, A:H.14, A:D.227 ZN.5: 5 residues within 4Å: Chain A: H.12, M.44, C.154, H.155, E.178 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:C.154, A:E.178, A:E.178, H2O.5 ZN.6: 4 residues within 4Å: Chain A: E.65, G.345, G.347, Q.348 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.345, A:G.347, H2O.7, H2O.8, H2O.8 ZN.7: 2 residues within 4Å: Chain A: H.275 Chain B: H.282 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.275, H2O.8, H2O.9 ZN.10: 8 residues within 4Å: Chain B: H.12, K.97, Y.99, T.103, H.131, H.155 Ligands: NCD.8, ZN.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.131, B:H.155 ZN.11: 9 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: NCD.8, ZN.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.12, B:H.14, B:D.227 ZN.12: 5 residues within 4Å: Chain B: H.12, M.44, C.154, H.155, E.178 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:C.154, B:E.178, B:E.178, H2O.14 ZN.13: 4 residues within 4Å: Chain B: E.65, G.345, G.347, Q.348 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.345, B:G.347, H2O.17, H2O.17, H2O.18 ZN.14: 2 residues within 4Å: Chain A: H.282 Chain B: H.275 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.275, H2O.18, H2O.18

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