SMTL ID : 1j79.1

Molecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a Binuclear Metal Center

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.16, H.18, K.102, D.250 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.16, A:H.18, A:D.250, H2O.11 ZN.2: 5 residues within 4Å: Chain A: K.102, H.139, H.177 Ligands: ZN.1, ORO.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.139, A:H.177, H2O.11 ZN.5: 6 residues within 4Å: Chain B: H.16, H.18, K.102, D.250 Ligands: ZN.6, NCD.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.16, B:H.18, B:D.250 ZN.6: 5 residues within 4Å: Chain B: K.102, H.139, H.177 Ligands: ZN.5, NCD.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.139, B:H.177

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 12 residues within 4Å: Chain A: H.18, R.20, N.44, H.139, C.221, L.222, D.250, A.252, H.254, A.266, G.267 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.44, A:L.222, A:L.222, A:A.266, A:A.266 Water bridges: A:R.20, A:A.266, A:C.268 Salt bridges: A:H.18, A:R.20, A:H.254

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

NCD.4: 6 residues within 4Å: Chain A: N.208, H.209, V.212, R.216 Chain B: A.145, R.152 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.208, A:N.208, A:R.216 Water bridges: A:N.206, B:R.152 Salt bridges: A:H.209, B:R.152 NCD.7: 15 residues within 4Å: Chain B: H.18, R.20, N.44, K.102, H.139, H.177, C.221, L.222, D.250, A.252, H.254, A.266, G.267 Ligands: ZN.5, ZN.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.44, B:L.222, B:L.222, B:A.266 Water bridges: B:R.20 Salt bridges: B:H.16, B:H.18, B:H.18, B:R.20, B:H.139, B:H.177, B:H.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Biochemistry (2001)

Release Date

2001-06-20

Peptides

dihydroorotase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

dihydroorotase