MolNFT v1 · #10925 · protein
Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center
1J79: “Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center”. X-ray diffraction, 3 ligands (NCD, ORO, ZN), 11 pockets (best druggability 0.64). MolNFT v1 #10925 on GenesisL1: 3D…
- PDB
- 1J79
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- P05020
- Ligands
- NCD, ORO, ZN
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase (EC 3.5.2.3) | protein | 343 | 38% helix, 17% strand | P05020 |
| B | Dihydroorotase (EC 3.5.2.3) | protein | 339 | 39% helix, 18% strand | P05020 |
Ligands and binding sites
- NCD · N-carbamoyl-L-aspartate · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.64 | 0.79 | 39 | NCD |
| 2 | 325 | 0.58 | 0.77 | 40 | ZN, ORO |
| 3 | 144 | 0.51 | 0.79 | 21 | empty |
| 4 | 128 | 0.44 | 0.77 | 26 | empty |
| 5 | 61 | 0.42 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1140 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 1J79 · Molecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a… · the same entry in another collection · chain A against A, TM-score 1.00
- P05020 · AlphaFold monomer V2.0 prediction for dihydroorotase (P05020) · a predicted model of the same protein · chain B against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05020
- Elsewhere: RCSB PDB 1J79 · PDBe 1J79 · UniProt P05020
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