MolNFT v1 · #71619 · protein
HIS257ALA mutant of dihydroorotase from E. COLI
3MJM: “HIS257ALA mutant of dihydroorotase from E. COLI”. X-ray diffraction, 4 ligands (DOR, NCD, CP), 8 pockets (best druggability 0.58). MolNFT v1 #71619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MJM
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- B1IV40
- Ligands
- DOR, NCD, CP, ZN
- Pockets
- 8 · best druggability 0.58
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 | 344 | 38% helix, 17% strand | B1IV40 |
| B | Dihydroorotase (EC 3.5.2.3) | protein | 343 | 38% helix, 17% strand | B1IV40 |
Ligands and binding sites
- DOR · (4S)-2,6-dioxohexahydropyrimidine-4-carboxylic acid · ligand · chains A
- NCD · N-carbamoyl-L-aspartate · ligand · chains B
- CP · Phosphoric acid mono(formamide)ester · ligand · chains A, B
- 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
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.58 | 0.77 | 39 | DOR |
| 2 | 116 | 0.47 | 0.79 | 20 | empty |
| 3 | 112 | 0.46 | 0.78 | 23 | empty |
| 4 | 115 | 0.44 | 0.77 | 16 | empty |
| 5 | 103 | 0.42 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1175 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
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 B1IV40
- Elsewhere: RCSB PDB 3MJM · PDBe 3MJM · UniProt B1IV40
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