Research workbench
Crystal structure of mycobacterium tuberculosis argf in complex with 2-fluoro-4-hydroxybenzonitrile.
Analyse Crystal structure of mycobacterium tuberculosis argf in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NOR
- 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
- P9WIT9
- Ligands
- 8H8, PO4
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 308 | 47% helix, 17% strand | P9WIT9 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 298 | 46% helix, 16% strand | P9WIT9 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 307 | 46% helix, 16% strand | P9WIT9 |
| D, E | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 299 | 45% helix, 16% strand | P9WIT9 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 299 | 45% helix, 17% strand | P9WIT9 |
Ligands and binding sites
- 8H8 · 2-fluoro-4-hydroxybenzonitrile · ligand · 4 copies · chains A, C, B, D, F, E
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.84 | 0.86 | 95 | PO4 |
| 2 | 380 | 0.75 | 0.86 | 53 | 8H8, PO4 |
| 3 | 310 | 0.73 | 0.86 | 50 | PO4, 8H8 |
| 4 | 248 | 0.73 | 0.88 | 39 | empty |
| 5 | 391 | 0.72 | 0.83 | 45 | PO4, 8H8 |
Interfaces
9 interfaces between chains.
- A–B · 1156 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1136 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1105 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1058 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1051 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7NOR · Crystal structure of Mycobacterium tuberculosis ArgF in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- P9WIT9 · AlphaFold monomer V2.0 prediction for ornithine carbamoyltransferase (P9WIT9) · a predicted model of the same protein · chain A 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 P9WIT9
- Elsewhere: RCSB PDB 7NOR · PDBe 7NOR · UniProt P9WIT9
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