SMTL ID : 8pbj.1

Mutant R1722W of the dihydroorotase domain of human CAD protein bound to the substrate carbamoyl aspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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.8, ZN.9 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.11: 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.18, ZN.19 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.46, B:T.103, B:T.103, B:R.202, B:R.202, B:P.243 Water bridges: B:D.227 Salt bridges: B:H.12, B:H.14, B:H.14, B:R.16, B:H.131, B:H.155, B:H.231

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

FMT.2: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.12 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.4: 2 residues within 4Å: Chain A: G.84, T.85 No protein-ligand interaction detected (PLIP) FMT.6: 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.7: 5 residues within 4Å: Chain A: R.4, P.6, T.289, Y.290 Chain B: Q.355 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.4, A:R.4, A:T.289 Water bridges: A:G.7 FMT.12: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.2 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.14: 2 residues within 4Å: Chain B: G.84, T.85 No protein-ligand interaction detected (PLIP) FMT.16: 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.17: 5 residues within 4Å: Chain A: Q.355 Chain B: R.4, P.6, T.289, Y.290 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.4, B:R.4, B:T.289 Water bridges: B:G.7

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: V.211, E.212, W.215, W.263 No protein-ligand interaction detected (PLIP) GOL.5: 5 residues within 4Å: Chain A: E.332, L.341, V.342, P.343, Y.346 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.332, A:L.341 Water bridges: A:V.333, A:V.333 GOL.13: 4 residues within 4Å: Chain B: V.211, E.212, W.215, W.263 No protein-ligand interaction detected (PLIP) GOL.15: 5 residues within 4Å: Chain B: E.332, L.341, V.342, P.343, Y.346 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.332, B:E.332, B:L.341 Water bridges: B:V.333, B:V.333

6 x ZN: ZINC ION(Non-covalent)

ZN.8: 9 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: NCD.1, ZN.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.12, A:H.14, A:D.227 ZN.9: 8 residues within 4Å: Chain A: H.12, K.97, Y.99, T.103, H.131, H.155 Ligands: NCD.1, ZN.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.131, A:H.155 ZN.10: 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.18: 9 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: NCD.11, ZN.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.12, B:H.14, B:D.227 ZN.19: 8 residues within 4Å: Chain B: H.12, K.97, Y.99, T.103, H.131, H.155 Ligands: NCD.11, ZN.18 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.131, B:H.155 ZN.20: 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.19

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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