SMTL ID : 8pbu.1

Mutant K1482M of the dihydroorotase domain of human CAD protein bound to the inhibitor fluoorotate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x FOT: 5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

FOT.1: 13 residues within 4Å: Chain A: H.14, R.16, N.46, K.97, Y.99, H.131, V.201, R.202, A.229, H.231, P.243, G.244 Ligands: ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.46, A:N.46, A:R.202, A:R.202, A:P.243 Salt bridges: A:H.14, A:R.16, A:H.231 Halogen bonds: A:N.46 FOT.15: 13 residues within 4Å: Chain B: H.14, R.16, N.46, K.97, Y.99, H.131, V.201, R.202, A.229, H.231, P.243, G.244 Ligands: ZN.17 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.46, B:N.46, B:R.202, B:R.202, B:P.243 Salt bridges: B:H.14, B:R.16, B:H.231 Halogen bonds: B:N.46

10 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.14, A:D.227, H2O.5 ZN.3: 7 residues within 4Å: Chain A: H.12, K.97, Y.99, H.131, H.155 Ligands: FOT.1, ZN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.5 ZN.4: 4 residues within 4Å: Chain A: H.282 Chain B: H.275 Ligands: FMT.12, FMT.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.282, B:H.275 ZN.5: 5 residues within 4Å: Chain A: H.22, H.231, E.235, P.242 Ligands: FMT.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.22, A:H.231, A:E.235, A:E.235 ZN.6: 5 residues within 4Å: Chain A: Q.355, A.357, V.358, P.359 Ligands: FMT.12 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.355, A:A.357, H2O.4, H2O.8 ZN.16: 7 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: ZN.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.14, B:D.227, H2O.15 ZN.17: 7 residues within 4Å: Chain B: H.12, K.97, Y.99, H.131, H.155 Ligands: FOT.15, ZN.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.15 ZN.18: 4 residues within 4Å: Chain A: H.275 Chain B: H.282 Ligands: FMT.26, FMT.28 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.275, B:H.282 ZN.19: 5 residues within 4Å: Chain B: H.22, H.231, E.235, P.242 Ligands: FMT.22 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.22, B:H.231, B:E.235, B:E.235 ZN.20: 5 residues within 4Å: Chain B: Q.355, A.357, V.358, P.359 Ligands: FMT.26 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Q.355, B:A.357, H2O.14, H2O.18

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

FMT.7: 6 residues within 4Å: Chain A: R.4, L.5, P.6, T.289, Y.290 Chain B: Q.355 Ligand excluded by PLIP FMT.8: 5 residues within 4Å: Chain A: H.22, H.231, E.235, P.242 Ligands: ZN.5 Ligand excluded by PLIP FMT.9: 7 residues within 4Å: Chain A: R.16, P.18, G.19, T.21, H.22, T.47, R.48 Ligand excluded by PLIP FMT.10: 8 residues within 4Å: Chain A: L.126, P.127, I.128, R.149, S.150, V.151, H.152, I.280 Ligand excluded by PLIP FMT.11: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.25 Ligand excluded by PLIP FMT.12: 12 residues within 4Å: Chain A: R.278, H.282, L.283, P.284, Q.355, A.357, P.359 Chain B: P.6, H.275 Ligands: ZN.4, ZN.6, FMT.14 Ligand excluded by PLIP FMT.13: 10 residues within 4Å: Chain A: R.16, H.22, M.23, E.24, P.230, H.231, T.232, E.235, K.309, A.310 Ligand excluded by PLIP FMT.14: 8 residues within 4Å: Chain A: H.282, P.359 Chain B: P.6, L.270, H.274, H.275 Ligands: ZN.4, FMT.12 Ligand excluded by PLIP FMT.21: 6 residues within 4Å: Chain A: Q.355 Chain B: R.4, L.5, P.6, T.289, Y.290 Ligand excluded by PLIP FMT.22: 5 residues within 4Å: Chain B: H.22, H.231, E.235, P.242 Ligands: ZN.19 Ligand excluded by PLIP FMT.23: 7 residues within 4Å: Chain B: R.16, P.18, G.19, T.21, H.22, T.47, R.48 Ligand excluded by PLIP FMT.24: 8 residues within 4Å: Chain B: L.126, P.127, I.128, R.149, S.150, V.151, H.152, I.280 Ligand excluded by PLIP FMT.25: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.11 Ligand excluded by PLIP FMT.26: 12 residues within 4Å: Chain A: P.6, H.275 Chain B: R.278, H.282, L.283, P.284, Q.355, A.357, P.359 Ligands: ZN.18, ZN.20, FMT.28 Ligand excluded by PLIP FMT.27: 10 residues within 4Å: Chain B: R.16, H.22, M.23, E.24, P.230, H.231, T.232, E.235, K.309, A.310 Ligand excluded by PLIP FMT.28: 8 residues within 4Å: Chain A: P.6, L.270, H.274, H.275 Chain B: H.282, P.359 Ligands: ZN.18, FMT.26 Ligand excluded by PLIP

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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