SMTL ID : 8pbe.1

Mutant K1556T of the dihydroorotase domain of human CAD protein bound to the substrate carbamoyl aspartate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

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

FMT.1: 10 residues within 4Å: Chain A: H.12, H.14, M.44, T.97, Y.99, H.131, H.155 Ligands: NCD.2, ZN.5, ZN.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.99, A:Y.99 FMT.3: 6 residues within 4Å: Chain A: P.127, I.128, R.149, S.150, V.151, H.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.128, A:I.128, A:R.149 Water bridges: A:S.150, A:S.150 FMT.4: 6 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278 Ligands: FMT.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.275, A:R.278, B:H.275, B:R.278 FMT.7: 10 residues within 4Å: Chain B: H.12, H.14, M.44, T.97, Y.99, H.131, H.155 Ligands: NCD.8, ZN.11, ZN.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.99, B:Y.99 FMT.9: 6 residues within 4Å: Chain B: P.127, I.128, R.149, S.150, V.151, H.152 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.128, B:I.128, B:R.149 Water bridges: B:S.150, B:S.150 FMT.10: 6 residues within 4Å: Chain A: H.275, R.278 Chain B: H.275, R.278, R.279 Ligands: FMT.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.275, A:R.278, B:H.275, B:R.278

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

NCD.2: 19 residues within 4Å: Chain A: H.12, H.14, R.16, N.46, 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: FMT.1, ZN.5, ZN.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.46, A:T.103, A:R.202, A:R.202, A:P.243, 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, 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: FMT.7, ZN.11, ZN.12 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.46, B:T.103, B:R.202, B:R.202, B:P.243, 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

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 8 residues within 4Å: Chain A: H.12, H.14, M.44, H.155, D.227 Ligands: FMT.1, NCD.2, ZN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.12, A:H.14, A:D.227 ZN.6: 8 residues within 4Å: Chain A: H.12, Y.99, T.103, H.131, H.155 Ligands: FMT.1, NCD.2, ZN.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.131, A:H.155 ZN.11: 8 residues within 4Å: Chain B: H.12, H.14, M.44, H.155, D.227 Ligands: FMT.7, NCD.8, ZN.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.12, B:H.14, B:D.227 ZN.12: 8 residues within 4Å: Chain B: H.12, Y.99, T.103, H.131, H.155 Ligands: FMT.7, NCD.8, ZN.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.131, B:H.155

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

Related Entries With Identical Sequence