SMTL ID : 8pbp.1

Mutant R1785C of the dihydroorotase domain of human CAD protein bound to the substrate carbamoyl aspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

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

NCD.1: 21 residues within 4Å: Chain A: H.12, H.14, R.16, N.46, K.97, Y.99, T.103, F.104, S.105, H.131, H.155, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: DOR.3, ZN.5, ZN.6 11 PLIP interactions: 11 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.14, A:H.14, A:R.16, A:H.131, A:H.155, A:H.231 NCD.8: 21 residues within 4Å: Chain B: H.12, H.14, R.16, N.46, K.97, Y.99, T.103, F.104, S.105, H.131, H.155, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: DOR.10, ZN.12, ZN.13 11 PLIP interactions: 11 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.14, B:H.14, B:R.16, B:H.131, B:H.155, B:H.231

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

FMT.2: 8 residues within 4Å: Chain A: L.126, P.127, I.128, V.129, R.149, S.150, V.151, H.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.128, A:R.149, A:S.150 Water bridges: A:S.150, A:S.150 FMT.4: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.275, B:R.278, A:H.275, A:R.278 FMT.9: 8 residues within 4Å: Chain B: L.126, P.127, I.128, V.129, R.149, S.150, V.151, H.152 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.128, B:R.149, B:S.150 Water bridges: B:S.150, B:S.150 FMT.11: 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 B, 2 interactions with chain A Hydrogen bonds: B:H.275, B:R.278, A:H.275, A:R.278

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

DOR.3: 19 residues within 4Å: Chain A: H.14, R.16, N.46, K.97, Y.99, T.103, F.104, S.105, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: NCD.1, ZN.5, ZN.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.46, A:R.202, A:R.202, A:P.243 Salt bridges: A:H.14, A:R.16, A:H.231 DOR.10: 19 residues within 4Å: Chain B: H.14, R.16, N.46, K.97, Y.99, T.103, F.104, S.105, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: NCD.8, ZN.12, ZN.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.46, B:R.202, B:R.202, B:P.243 Salt bridges: B:H.14, B:R.16, B:H.231

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 9 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: NCD.1, DOR.3, ZN.6 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.6: 8 residues within 4Å: Chain A: H.12, K.97, Y.99, H.131, H.155 Ligands: NCD.1, DOR.3, ZN.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.2 ZN.7: 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.8, H2O.8, H2O.9 ZN.12: 9 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: NCD.8, DOR.10, 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.11 ZN.13: 8 residues within 4Å: Chain B: H.12, K.97, Y.99, H.131, H.155 Ligands: NCD.8, DOR.10, ZN.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.11 ZN.14: 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.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