SMTL ID : 9fs3.1

Mutant S1538A of the dihydroorotase domain of human CAD protein in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

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

FMT.1: 6 residues within 4Å: Chain A: F.185, L.254, T.257, Q.318, K.319, V.320 Ligand excluded by PLIP FMT.2: 4 residues within 4Å: Chain A: R.4, P.6, T.289, Y.290 Ligand excluded by PLIP FMT.3: 5 residues within 4Å: Chain A: G.84, T.85, L.86, G.87, T.88 Ligand excluded by PLIP FMT.4: 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.5: 3 residues within 4Å: Chain A: H.297, W.299, T.323 Ligand excluded by PLIP FMT.6: 2 residues within 4Å: Chain A: H.275 Ligands: ZN.13 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain A: R.171, L.173 Chain B: M.142, Q.145, L.146 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: H.275, R.278, R.279 Ligand excluded by PLIP FMT.9: 4 residues within 4Å: Chain A: P.18, P.49, L.59, L.63 Ligand excluded by PLIP FMT.16: 6 residues within 4Å: Chain B: F.185, L.254, T.257, Q.318, K.319, V.320 Ligand excluded by PLIP FMT.17: 4 residues within 4Å: Chain B: R.4, P.6, T.289, Y.290 Ligand excluded by PLIP FMT.18: 5 residues within 4Å: Chain B: G.84, T.85, L.86, G.87, T.88 Ligand excluded by PLIP FMT.19: 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.20: 3 residues within 4Å: Chain B: H.297, W.299, T.323 Ligand excluded by PLIP FMT.21: 2 residues within 4Å: Chain B: H.275 Ligands: ZN.28 Ligand excluded by PLIP FMT.22: 5 residues within 4Å: Chain A: M.142, Q.145, L.146 Chain B: R.171, L.173 Ligand excluded by PLIP FMT.23: 3 residues within 4Å: Chain B: H.275, R.278, R.279 Ligand excluded by PLIP FMT.24: 4 residues within 4Å: Chain B: P.18, P.49, L.59, L.63 Ligand excluded by PLIP

8 x ZN: ZINC ION(Non-covalent)

ZN.10: 6 residues within 4Å: Chain A: H.12, K.97, Y.99, H.131, H.155 Ligands: ZN.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:H.155, H2O.6 ZN.11: 8 residues within 4Å: Chain A: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: ZN.10, GOL.14 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.14, A:D.227, H2O.6 ZN.12: 5 residues within 4Å: Chain A: H.12, M.44, C.154, H.155, E.178 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:C.154, A:E.178, H2O.7 ZN.13: 2 residues within 4Å: Chain A: H.275 Ligands: FMT.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.275, H2O.13 ZN.25: 6 residues within 4Å: Chain B: H.12, K.97, Y.99, H.131, H.155 Ligands: ZN.26 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.131, B:H.155, H2O.23 ZN.26: 8 residues within 4Å: Chain B: H.12, H.14, M.44, K.97, H.155, D.227 Ligands: ZN.25, GOL.29 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.14, B:D.227, H2O.23 ZN.27: 5 residues within 4Å: Chain B: H.12, M.44, C.154, H.155, E.178 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:C.154, B:E.178, H2O.24 ZN.28: 2 residues within 4Å: Chain B: H.275 Ligands: FMT.21 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.275, H2O.30

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 11 residues within 4Å: Chain A: H.14, R.16, N.46, R.202, D.227, A.229, H.231, P.242, P.243, G.244 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.16, A:R.16, A:N.46, A:H.231 GOL.29: 11 residues within 4Å: Chain B: H.14, R.16, N.46, R.202, D.227, A.229, H.231, P.242, P.243, G.244 Ligands: ZN.26 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.16, B:R.16, B:N.46, B:H.231

2 x NA: SODIUM ION(Non-functional Binders)

NA.15: 4 residues within 4Å: Chain A: E.65, G.345, G.347, Q.348 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.345 NA.30: 4 residues within 4Å: Chain B: E.65, G.345, G.347, Q.348 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.345

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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