SMTL ID : 9fs2.1

Mutant S1538A of the dihydroorotase domain of human CAD protein bound to substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 10 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: ZN.2, NCD.3, DOR.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.14, A:D.227, H2O.9 ZN.2: 9 residues within 4Å: Chain A: H.12, K.97, Y.99, T.103, H.131, H.155 Ligands: ZN.1, NCD.3, DOR.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.9 ZN.4: 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.8 ZN.13: 2 residues within 4Å: Chain A: H.282 Chain B: H.275 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.282, B:H.275, H2O.14, H2O.15 ZN.18: 10 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, Y.99, H.155, D.227 Ligands: ZN.19, NCD.20, DOR.22 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.14, B:D.227, H2O.28 ZN.19: 9 residues within 4Å: Chain B: H.12, K.97, Y.99, T.103, H.131, H.155 Ligands: ZN.18, NCD.20, DOR.22 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.28 ZN.21: 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.27 ZN.30: 2 residues within 4Å: Chain A: H.275 Chain B: H.282 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.275, B:H.282, H2O.34, H2O.34

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

NCD.3: 20 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.1, ZN.2, DOR.5 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.20: 20 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, DOR.22 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 DOR: (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

DOR.5: 18 residues within 4Å: Chain A: H.14, R.16, N.46, K.97, Y.99, T.103, F.104, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.1, ZN.2, NCD.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.104 Hydrogen bonds: A:N.46, A:T.103, A:R.202, A:R.202, A:P.243 Water bridges: A:F.245 Salt bridges: A:H.14, A:R.16, A:H.231 DOR.22: 18 residues within 4Å: Chain B: H.14, R.16, N.46, K.97, Y.99, T.103, F.104, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.18, ZN.19, NCD.20 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.104 Hydrogen bonds: B:N.46, B:T.103, B:R.202, B:R.202, B:P.243 Water bridges: B:F.245 Salt bridges: B:H.14, B:R.16, B:H.231

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

FMT.6: 7 residues within 4Å: Chain A: P.127, I.128, V.129, R.149, S.150, V.151, H.152 Ligand excluded by PLIP FMT.7: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.24 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: M.142, Q.145, L.146 Ligand excluded by PLIP FMT.9: 6 residues within 4Å: Chain A: F.185, L.254, T.257, Q.318, K.319, V.320 Ligand excluded by PLIP FMT.10: 1 residues within 4Å: Chain A: S.239 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain A: R.4, Y.290, E.292, R.326 Ligand excluded by PLIP FMT.12: 4 residues within 4Å: Chain A: A.357, V.358, P.359, Q.360 Ligand excluded by PLIP FMT.14: 7 residues within 4Å: Chain A: R.69, Q.339, V.340, L.341, V.342, P.343, P.344 Ligand excluded by PLIP FMT.15: 2 residues within 4Å: Chain A: D.53, P.55 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain A: R.4, P.6, T.289, Y.290 Chain B: Q.355 Ligand excluded by PLIP FMT.17: 2 residues within 4Å: Chain B: S.124, H.125 Ligand excluded by PLIP FMT.23: 7 residues within 4Å: Chain B: P.127, I.128, V.129, R.149, S.150, V.151, H.152 Ligand excluded by PLIP FMT.24: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.7 Ligand excluded by PLIP FMT.25: 3 residues within 4Å: Chain B: M.142, Q.145, L.146 Ligand excluded by PLIP FMT.26: 6 residues within 4Å: Chain B: F.185, L.254, T.257, Q.318, K.319, V.320 Ligand excluded by PLIP FMT.27: 1 residues within 4Å: Chain B: S.239 Ligand excluded by PLIP FMT.28: 4 residues within 4Å: Chain B: R.4, Y.290, E.292, R.326 Ligand excluded by PLIP FMT.29: 4 residues within 4Å: Chain B: A.357, V.358, P.359, Q.360 Ligand excluded by PLIP FMT.31: 7 residues within 4Å: Chain B: R.69, Q.339, V.340, L.341, V.342, P.343, P.344 Ligand excluded by PLIP FMT.32: 2 residues within 4Å: Chain B: D.53, P.55 Ligand excluded by PLIP FMT.33: 5 residues within 4Å: Chain A: Q.355 Chain B: R.4, P.6, T.289, Y.290 Ligand excluded by PLIP FMT.34: 2 residues within 4Å: Chain A: S.124, H.125 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Del Cano-Ochoa, F. et al., Disruption of CAD Oligomerization by Pathogenic Variants. J.Mol.Biol. (2024)

Release Date

2024-12-04

Peptides

Multifunctional protein CAD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Multifunctional protein CAD

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