Research workbench
Crystal structure of anabolic ornithine carbamoyltransferase from vibrio vulnificus in complex with citrulline and inorganic phosphate
Analyse Crystal structure of anabolic ornithine carbamoyltransferase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JQO
- Type
- protein
- Length
- 1,012 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine carbamoyltransferase
- EC
- 2.1.3.3
- UniProt
- Q8DCF5
- Ligands
- CIR, PO4, CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 338 | 49% helix, 15% strand | Q8DCF5 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 340 | 48% helix, 14% strand | Q8DCF5 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 334 | 48% helix, 14% strand | Q8DCF5 |
Ligands and binding sites
- CIR · Citrulline · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.77 | 0.90 | 41 | empty |
| 2 | 75 | 0.72 | 0.97 | 22 | PO4, CIR |
| 3 | 77 | 0.72 | 0.96 | 23 | PO4, CIR |
| 4 | 75 | 0.72 | 0.96 | 23 | PO4, CIR |
| 5 | 342 | 0.57 | 0.76 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1368 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1365 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1351 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4JQO · Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DCF5 · AlphaFold monomer V2.0 prediction for ornithine carbamoyltransferase (Q8DCF5) · a predicted model of the same protein · chain C 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 Q8DCF5
- Elsewhere: RCSB PDB 4JQO · PDBe 4JQO · UniProt Q8DCF5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.