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Crystal structure of anabolic ornithine carbamoyltransferase from campylobacter jejuni subsp. jejuni nctc 11168
Analyse Crystal structure of anabolic ornithine carbamoyltransferase from campylobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TPF
- Type
- protein
- Length
- 1,810 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine carbamoyltransferase
- EC
- 2.1.3.3
- UniProt
- Q9PNU6
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 303 | 50% helix, 16% strand | Q9PNU6 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 305 | 50% helix, 16% strand | Q9PNU6 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 301 | 49% helix, 16% strand | Q9PNU6 |
| E | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 300 | 49% helix, 16% strand | Q9PNU6 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 298 | 50% helix, 16% strand | Q9PNU6 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.83 | 0.84 | 127 | empty |
| 2 | 873 | 0.81 | 0.83 | 94 | empty |
| 3 | 472 | 0.72 | 0.82 | 50 | empty |
| 4 | 403 | 0.70 | 0.81 | 53 | empty |
| 5 | 333 | 0.69 | 0.83 | 50 | empty |
Interfaces
10 interfaces between chains.
- B–C · 985 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 977 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 975 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 924 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 77 modified (engineered).
Compared structures
- 3TPF · Crystal structure of anabolic ornithine carbamoyltransferase from Campylobacter jejuni… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9PNU6 · AlphaFold monomer V2.0 prediction for ornithine carbamoyltransferase, anabolic (Q9PNU6) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 Q9PNU6
- Elsewhere: RCSB PDB 3TPF · PDBe 3TPF · UniProt Q9PNU6
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