SMTL ID : 4c6f.1

Crystal structure of the dihydroorotase domain of human CAD bound to substrate at pH 6.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

homo-dimer

Ligands

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

DOR.1: 18 residues within 4Å: Chain A: H.20, R.22, N.52, K.103, Y.105, T.109, F.110, H.137, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: NCD.2, ZN.4, ZN.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.52, A:R.208, A:R.208, A:P.249 Water bridges: A:F.251 Salt bridges: A:H.20, A:R.22, A:H.237 DOR.11: 18 residues within 4Å: Chain B: H.20, R.22, N.52, K.103, Y.105, T.109, F.110, H.137, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: NCD.12, ZN.14, ZN.15 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.52, B:R.208, B:R.208, B:P.249 Water bridges: B:F.251 Salt bridges: B:H.20, B:R.22, B:H.237

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

NCD.2: 20 residues within 4Å: Chain A: H.18, H.20, R.22, N.52, K.103, Y.105, T.109, F.110, H.137, H.161, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: DOR.1, ZN.4, ZN.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.52, A:T.109, A:R.208, A:D.233, A:P.249 Salt bridges: A:H.18, A:H.20, A:H.20, A:R.22, A:H.137, A:H.161, A:H.237 NCD.12: 20 residues within 4Å: Chain B: H.18, H.20, R.22, N.52, K.103, Y.105, T.109, F.110, H.137, H.161, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: DOR.11, ZN.14, ZN.15 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.52, B:T.109, B:R.208, B:D.233, B:P.249 Water bridges: B:D.233 Salt bridges: B:H.18, B:H.20, B:H.20, B:R.22, B:H.137, B:H.161, B:H.237

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.18, M.50, C.160, H.161, E.184 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, A:C.160, A:E.184, H2O.3 ZN.4: 9 residues within 4Å: Chain A: H.18, H.20, M.50, K.103, H.161, D.233 Ligands: DOR.1, NCD.2, ZN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, A:H.20, A:D.233, H2O.3 ZN.5: 9 residues within 4Å: Chain A: H.18, K.103, Y.105, T.109, H.137, H.161 Ligands: DOR.1, NCD.2, ZN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.137, A:H.161, H2O.3 ZN.7: 1 residues within 4Å: Chain A: H.288 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.288, H2O.12 ZN.13: 5 residues within 4Å: Chain B: H.18, M.50, C.160, H.161, E.184 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.18, B:C.160, B:E.184, H2O.18 ZN.14: 9 residues within 4Å: Chain B: H.18, H.20, M.50, K.103, H.161, D.233 Ligands: DOR.11, NCD.12, ZN.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.18, B:H.20, B:D.233, H2O.18 ZN.15: 9 residues within 4Å: Chain B: H.18, K.103, Y.105, T.109, H.137, H.161 Ligands: DOR.11, NCD.12, ZN.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.137, B:H.161, H2O.18 ZN.17: 1 residues within 4Å: Chain B: H.288 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.288, H2O.27

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

FMT.6: 7 residues within 4Å: Chain A: P.133, I.134, V.135, R.155, S.156, V.157, H.158 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.134, A:I.134, A:R.155 Water bridges: A:S.156, A:S.156, A:T.182 FMT.8: 3 residues within 4Å: Chain A: H.281, R.284, R.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.281, A:R.284 FMT.9: 4 residues within 4Å: Chain A: R.10, P.12, T.295, Y.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.10, A:R.10 Water bridges: A:G.13 FMT.10: 6 residues within 4Å: Chain A: Q.151, R.177, L.179 Chain B: M.148, Q.151, L.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.177, A:R.177 FMT.16: 7 residues within 4Å: Chain B: P.133, I.134, V.135, R.155, S.156, V.157, H.158 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.134, B:I.134, B:R.155 Water bridges: B:S.156, B:S.156, B:T.182 FMT.18: 3 residues within 4Å: Chain B: H.281, R.284, R.285 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.281, B:R.284 FMT.19: 4 residues within 4Å: Chain B: R.10, P.12, T.295, Y.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.10, B:R.10 Water bridges: B:G.13 FMT.20: 6 residues within 4Å: Chain A: M.148, Q.151, L.152 Chain B: Q.151, R.177, L.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.177, B:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grande-Garcia, A. et al., Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad. Structure (2014)

Release Date

2014-02-05

Peptides

DIHYDROOROTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DIHYDROOROTASE

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