SMTL ID : 6hfr.1

Human dihydroorotase mutant F1563Y co-crystallized with carbamoyl aspartate at pH 7.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.18, K.103, Y.105, T.109, H.137, H.161 Ligands: ZN.2, NCD.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.137, A:H.161 ZN.2: 8 residues within 4Å: Chain A: H.18, H.20, M.50, K.103, H.161, D.233 Ligands: ZN.1, NCD.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.18, A:H.20, A:D.233 ZN.3: 5 residues within 4Å: Chain A: H.18, M.50, C.160, H.161, E.184 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, A:C.160, A:E.184, A:E.184, H2O.5 ZN.8: 2 residues within 4Å: Chain A: H.281 Chain B: H.288 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.281, H2O.11, H2O.12 ZN.9: 8 residues within 4Å: Chain B: H.18, K.103, Y.105, T.109, H.137, H.161 Ligands: ZN.10, NCD.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.137, B:H.161 ZN.10: 8 residues within 4Å: Chain B: H.18, H.20, M.50, K.103, H.161, D.233 Ligands: ZN.9, NCD.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.18, B:H.20, B:D.233 ZN.11: 5 residues within 4Å: Chain B: H.18, M.50, C.160, H.161, E.184 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.18, B:C.160, B:E.184, B:E.184, H2O.18 ZN.16: 2 residues within 4Å: Chain A: H.288 Chain B: H.281 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.281, H2O.25, H2O.26

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

NCD.4: 19 residues within 4Å: Chain A: H.18, H.20, R.22, N.52, K.103, Y.105, T.109, Y.110, H.137, H.161, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.52, A:T.109, A:R.208, A:R.208, 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: 19 residues within 4Å: Chain B: H.18, H.20, R.22, N.52, K.103, Y.105, T.109, Y.110, H.137, H.161, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: ZN.9, ZN.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.52, B:T.109, B:R.208, B:R.208, B:P.249 Salt bridges: B:H.18, B:H.20, B:H.20, B:R.22, B:H.137, B:H.161, B:H.237

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

FMT.5: 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.6: 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.7: 7 residues within 4Å: Chain A: H.281, R.284, R.285 Chain B: H.281, R.284, R.285 Ligands: FMT.15 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.13: 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.14: 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 FMT.15: 7 residues within 4Å: Chain A: H.281, R.284, R.285 Chain B: H.281, R.284, R.285 Ligands: FMT.7 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

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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