SMTL ID : 8pbt.1

Mutant K1482M of the dihydroorotase domain of human CAD protein bound to the substrate dihydroorotate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: A.31, R.69, F.307, G.338, Q.339, V.340 Ligands: FMT.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.340 GOL.22: 7 residues within 4Å: Chain B: A.31, R.69, F.307, G.338, Q.339, V.340 Ligands: FMT.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.340

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

DOR.2: 15 residues within 4Å: Chain A: H.14, R.16, N.46, K.97, Y.99, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.4, ZN.7 8 PLIP interactions: 8 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 DOR.23: 15 residues within 4Å: Chain B: H.14, R.16, N.46, K.97, Y.99, H.131, V.201, R.202, D.227, A.229, H.231, P.243, G.244 Ligands: ZN.25, ZN.28 8 PLIP interactions: 8 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

14 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.22, H.231, E.235, P.242 Ligands: FMT.17 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.22, A:H.231, A:E.235, A:E.235 ZN.4: 7 residues within 4Å: Chain A: H.12, K.97, Y.99, H.131, H.155 Ligands: DOR.2, ZN.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.4 ZN.5: 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.6: 4 residues within 4Å: Chain A: H.282 Chain B: H.275 Ligands: FMT.14, FMT.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.275, A:H.282 ZN.7: 8 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: DOR.2, ZN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.14, A:D.227, H2O.4 ZN.8: 3 residues within 4Å: Chain A: D.294, H.297, R.325 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.294, A:H.297, H2O.10, H2O.10 ZN.9: 5 residues within 4Å: Chain A: Q.355, G.356, A.357, P.359 Ligands: FMT.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.355, A:A.357, H2O.4, H2O.7 ZN.24: 5 residues within 4Å: Chain B: H.22, H.231, E.235, P.242 Ligands: FMT.38 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.22, B:H.231, B:E.235, B:E.235 ZN.25: 7 residues within 4Å: Chain B: H.12, K.97, Y.99, H.131, H.155 Ligands: DOR.23, ZN.28 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.17 ZN.26: 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.18 ZN.27: 4 residues within 4Å: Chain A: H.275 Chain B: H.282 Ligands: FMT.35, FMT.36 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.275, B:H.282 ZN.28: 8 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: DOR.23, ZN.25 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.14, B:D.227, H2O.17 ZN.29: 3 residues within 4Å: Chain B: D.294, H.297, R.325 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.294, B:H.297, H2O.23, H2O.23 ZN.30: 5 residues within 4Å: Chain B: Q.355, G.356, A.357, P.359 Ligands: FMT.36 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Q.355, B:A.357, H2O.17, H2O.20

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

FMT.10: 5 residues within 4Å: Chain A: R.4, P.6, T.289, Y.290 Chain B: Q.355 Ligand excluded by PLIP FMT.11: 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.12: 8 residues within 4Å: Chain A: P.127, I.128, V.129, R.149, S.150, V.151, H.152, I.280 Ligand excluded by PLIP FMT.13: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.34 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.6, FMT.15 Ligand excluded by PLIP FMT.15: 12 residues within 4Å: Chain A: H.282, L.283, P.284, Q.355, G.356, A.357, V.358, P.359 Chain B: H.275 Ligands: ZN.6, ZN.9, FMT.14 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain A: R.16, E.17, P.18, G.19, D.25 Ligand excluded by PLIP FMT.17: 5 residues within 4Å: Chain A: H.22, H.231, E.235, P.242 Ligands: ZN.3 Ligand excluded by PLIP FMT.18: 9 residues within 4Å: Chain A: H.22, M.23, E.24, P.230, H.231, T.232, E.235, K.309, A.310 Ligand excluded by PLIP FMT.19: 7 residues within 4Å: Chain A: A.27, S.28, A.31, R.69, F.307, K.309 Ligands: GOL.1 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain A: T.103, F.104, S.105, R.108 Ligand excluded by PLIP FMT.21: 6 residues within 4Å: Chain A: F.185, L.254, T.257, Q.318, K.319, V.320 Ligand excluded by PLIP FMT.31: 5 residues within 4Å: Chain A: Q.355 Chain B: R.4, P.6, T.289, Y.290 Ligand excluded by PLIP FMT.32: 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.33: 8 residues within 4Å: Chain B: P.127, I.128, V.129, R.149, S.150, V.151, H.152, I.280 Ligand excluded by PLIP FMT.34: 7 residues within 4Å: Chain A: H.275, R.278, R.279 Chain B: H.275, R.278, R.279 Ligands: FMT.13 Ligand excluded by PLIP FMT.35: 8 residues within 4Å: Chain A: P.6, L.270, H.274, H.275 Chain B: H.282, P.359 Ligands: ZN.27, FMT.36 Ligand excluded by PLIP FMT.36: 12 residues within 4Å: Chain A: H.275 Chain B: H.282, L.283, P.284, Q.355, G.356, A.357, V.358, P.359 Ligands: ZN.27, ZN.30, FMT.35 Ligand excluded by PLIP FMT.37: 5 residues within 4Å: Chain B: R.16, E.17, P.18, G.19, D.25 Ligand excluded by PLIP FMT.38: 5 residues within 4Å: Chain B: H.22, H.231, E.235, P.242 Ligands: ZN.24 Ligand excluded by PLIP FMT.39: 9 residues within 4Å: Chain B: H.22, M.23, E.24, P.230, H.231, T.232, E.235, K.309, A.310 Ligand excluded by PLIP FMT.40: 7 residues within 4Å: Chain B: A.27, S.28, A.31, R.69, F.307, K.309 Ligands: GOL.22 Ligand excluded by PLIP FMT.41: 4 residues within 4Å: Chain B: T.103, F.104, S.105, R.108 Ligand excluded by PLIP FMT.42: 6 residues within 4Å: Chain B: F.185, L.254, T.257, Q.318, K.319, V.320 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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