MolNFT v1 · #87611 · protein
Crystal structure of the dihydroorotase domain of human cad bound to substrate at pH 6.5
4C6F: “Crystal structure of the dihydroorotase domain of human cad bound to substrate at pH 6.5”. X-ray diffraction, 3 ligands (DOR, NCD, ZN), 2 pockets (best druggability 0.40). MolNFT v1 #87611 on GenesisL1: 3D structure, binding sites…
- PDB
- 4C6F
- Type
- protein
- Length
- 364 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- P27708
- Ligands
- DOR, NCD, ZN
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase (EC 3.5.2.3) | protein | 364 | 35% helix, 20% strand | P27708 |
Ligands and binding sites
- DOR · (4S)-2,6-dioxohexahydropyrimidine-4-carboxylic acid · ligand · chains A
- NCD · N-carbamoyl-L-aspartate · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A
- FMT · Formic acid · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.40 | 0.78 | 17 | empty |
| 2 | 63 | 0.33 | 0.77 | 17 | FMT |
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 4C6F · Crystal structure of the dihydroorotase domain of human CAD bound to substrate at pH 6.5 · the same entry in another collection · chain A against A, TM-score 1.00
- P27708 · AlphaFold monomer V2.0 prediction for cad protein (P27708) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P27708
- Elsewhere: RCSB PDB 4C6F · PDBe 4C6F · UniProt P27708
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