Research workbench
Crystal structure of anabolic ornithine carbamoyltransferase from vibrio vulnificus in complex with carbamoyl phosphate and L-norvaline
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
- 4H31
- Type
- protein
- Length
- 1,002 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
- NVA, CP, CL
- Pockets
- 10 · best druggability 0.74
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 | 335 | 49% helix, 14% strand | Q8DCF5 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 333 | 49% helix, 14% strand | Q8DCF5 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 334 | 49% helix, 14% strand | Q8DCF5 |
Ligands and binding sites
- NVA · Norvaline · ligand · 3 copies · chains A, B, C
- CP · Phosphoric acid mono(formamide)ester · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 18 copies · chains A, C, B
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 3 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 | 271 | 0.74 | 0.88 | 40 | empty |
| 2 | 68 | 0.72 | 0.97 | 23 | NVA, CP |
| 3 | 91 | 0.66 | 0.92 | 29 | NVA, CP, PE5 |
| 4 | 96 | 0.65 | 0.90 | 29 | NVA, CP, PE5 |
| 5 | 319 | 0.56 | 0.76 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1372 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1369 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1356 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4H31 · Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8DCF5 · AlphaFold monomer V2.0 prediction for ornithine carbamoyltransferase (Q8DCF5) · a predicted model of the same protein · chain B 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 4H31 · PDBe 4H31 · UniProt Q8DCF5
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