Research workbench
Crystal structure of anabolic ornithine carbamoyltransferase from vibrio vulnificus in complex with carbamoyl 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
- 4JFR
- Type
- protein
- Length
- 1,010 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
- CP, MG, CL
- Pockets
- 7 · best druggability 0.80
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 | 336 | 49% helix, 14% strand | Q8DCF5 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 340 | 48% helix, 15% strand | Q8DCF5 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 334 | 49% helix, 15% strand | Q8DCF5 |
Ligands and binding sites
- CP · Phosphoric acid mono(formamide)ester · ligand · 2 copies · chains A, B, C
- MG · Magnesium ion · metal · chains B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.80 | 0.82 | 85 | empty |
| 2 | 280 | 0.71 | 0.85 | 46 | CP |
| 3 | 221 | 0.71 | 0.87 | 40 | CP |
| 4 | 338 | 0.57 | 0.76 | 57 | MG |
| 5 | 55 | 0.28 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1313 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1254 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1089 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4JFR · 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 4JFR · PDBe 4JFR · UniProt Q8DCF5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.