Research workbench
Crystal structure of unliganded anabolic ornithine carbamoyltransferase from vibrio vulnificus at 1.86 a resolution
Analyse Crystal structure of unliganded anabolic ornithine carbamoyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KWT
- Type
- protein
- Length
- 978 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
- CL
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 323 | 50% helix, 15% strand | Q8DCF5 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 327 | 48% helix, 15% strand | Q8DCF5 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 328 | 49% helix, 15% strand | Q8DCF5 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.83 | 0.84 | 117 | CL |
| 2 | 461 | 0.71 | 0.81 | 48 | CL |
| 3 | 338 | 0.56 | 0.76 | 44 | empty |
| 4 | 50 | 0.26 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1085 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1070 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1067 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4KWT · Crystal structure of unliganded anabolic ornithine carbamoyltransferase from Vibrio… · 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 4KWT · PDBe 4KWT · UniProt Q8DCF5
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