SMTL ID : 6hfj.1

Human dihydroorotase mutant F1563A co-crystallized with carbamoyl aspartate at pH 7.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.18, K.103, Y.105, H.137, H.161 Ligands: ZN.2, DOR.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.137, A:H.161, H2O.5 ZN.2: 9 residues within 4Å: Chain A: H.18, H.20, M.50, K.103, Y.105, H.161, D.233 Ligands: ZN.1, DOR.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, A:H.20, A:D.233, H2O.5 ZN.3: 4 residues within 4Å: Chain A: H.18, M.50, C.160, 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.7 ZN.4: 2 residues within 4Å: Chain A: H.281 Chain B: H.288 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.288, A:H.281, H2O.12, H2O.13 ZN.9: 7 residues within 4Å: Chain B: H.18, K.103, Y.105, H.137, H.161 Ligands: ZN.10, DOR.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.137, B:H.161, H2O.23 ZN.10: 9 residues within 4Å: Chain B: H.18, H.20, M.50, K.103, Y.105, H.161, D.233 Ligands: ZN.9, DOR.16 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.18, B:H.20, B:D.233, H2O.23 ZN.11: 4 residues within 4Å: Chain B: H.18, M.50, C.160, 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.24 ZN.12: 2 residues within 4Å: Chain A: H.288 Chain B: H.281 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.281, A:H.288, H2O.30, H2O.30

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

FMT.5: 8 residues within 4Å: Chain A: P.133, I.134, V.135, R.155, S.156, V.157, H.158, T.182 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.6: 7 residues within 4Å: Chain A: H.281, R.284, R.285 Chain B: H.281, R.284, R.285 Ligands: FMT.14 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.281, A:R.284, B:H.281, B:R.284 FMT.7: 5 residues within 4Å: Chain A: R.10, P.12, T.295, Y.296 Chain B: Q.361 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.10, A:R.10 Water bridges: A:G.13, A:T.295, A:T.295 FMT.13: 8 residues within 4Å: Chain B: P.133, I.134, V.135, R.155, S.156, V.157, H.158, T.182 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.14: 7 residues within 4Å: Chain A: H.281, R.284, R.285 Chain B: H.281, R.284, R.285 Ligands: FMT.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.281, A:R.284, B:H.281, B:R.284 FMT.15: 5 residues within 4Å: Chain A: Q.361 Chain B: R.10, P.12, T.295, Y.296 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.10, B:R.10 Water bridges: B:G.13, B:T.295, B:T.295

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

DOR.8: 15 residues within 4Å: Chain A: H.20, R.22, N.52, K.103, Y.105, H.137, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: ZN.1, ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.52, A:N.52, A:R.208, A:R.208, A:P.249 Water bridges: A:H.237, A:H.237 Salt bridges: A:H.20, A:R.22, A:H.237 DOR.16: 15 residues within 4Å: Chain B: H.20, R.22, N.52, K.103, Y.105, H.137, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: ZN.9, ZN.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.52, B:N.52, B:R.208, B:R.208, B:P.249 Water bridges: B:H.237, B:H.237 Salt bridges: B:H.20, B:R.22, B:H.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Del Cano-Ochoa, F. et al., Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD. J. Biol. Chem. (2018)

Release Date

2018-10-24

Peptides

CAD protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CAD protein

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