SMTL ID : 4c6n.1

Crystal structure of the dihydroorotase domain of human CAD E1637T mutant bound to substrate at pH 6.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: K.103, 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: 6 residues within 4Å: Chain A: H.18, H.20, K.103, 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.7: 5 residues within 4Å: Chain B: K.103, H.137, H.161 Ligands: ZN.8, NCD.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.137, B:H.161 ZN.8: 6 residues within 4Å: Chain B: H.18, H.20, K.103, D.233 Ligands: ZN.7, NCD.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.18, B:H.20, B:D.233

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

FMT.3: 6 residues within 4Å: Chain A: P.133, I.134, R.155, S.156, V.157, H.158 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.134, A:R.155, A:V.157 Water bridges: A:S.156, A:S.156 FMT.5: 2 residues within 4Å: Chain A: H.281, R.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.281, A:R.284 FMT.6: 7 residues within 4Å: Chain A: V.17, H.18, M.50, V.135, H.158, C.160, T.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.184 FMT.9: 6 residues within 4Å: Chain B: P.133, I.134, R.155, S.156, V.157, H.158 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.134, B:R.155, B:V.157 Water bridges: B:S.156, B:S.156 FMT.11: 2 residues within 4Å: Chain B: H.281, R.284 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.281, B:R.284 FMT.12: 7 residues within 4Å: Chain B: V.17, H.18, M.50, V.135, H.158, C.160, T.184 No protein-ligand interaction detected (PLIP)

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

NCD.4: 18 residues within 4Å: Chain A: H.18, H.20, R.22, N.52, K.103, T.109, F.110, H.137, H.161, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: ZN.1, ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.52, 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.10: 18 residues within 4Å: Chain B: H.18, H.20, R.22, N.52, K.103, T.109, F.110, H.137, H.161, V.207, R.208, D.233, A.235, H.237, P.249, G.250 Ligands: ZN.7, ZN.8 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

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

CAD PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CAD PROTEIN