Research workbench
Crystal structure of mycobacterium tuberculosis argf in complex with (4-methyl-3-NITROPHENYL)BORONIC acid.
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
- 7NOV
- Type
- protein
- Length
- 1,802 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
- UK2, PO4
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 302 | 47% helix, 17% strand | P9WIT9 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 294 | 46% helix, 18% strand | P9WIT9 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 307 | 46% helix, 17% strand | P9WIT9 |
| D | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 298 | 46% helix, 17% strand | P9WIT9 |
| E | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 301 | 47% helix, 17% strand | P9WIT9 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 300 | 46% helix, 17% strand | P9WIT9 |
Ligands and binding sites
- UK2 · (4-methyl-3-nitro-phenyl)-oxidanyl-oxidanylidene-boron · ligand · 8 copies · chains A, C, B, D, E, F
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.87 | 0.88 | 90 | PO4 |
| 2 | 502 | 0.74 | 0.83 | 48 | PO4, UK2 |
| 3 | 525 | 0.74 | 0.82 | 54 | PO4, UK2 |
| 4 | 449 | 0.73 | 0.83 | 50 | UK2 |
| 5 | 393 | 0.73 | 0.84 | 47 | UK2, PO4 |
Interfaces
9 interfaces between chains.
- A–B · 987 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 976 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 944 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 941 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 939 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7NOV · Crystal structure of Mycobacterium tuberculosis ArgF in complex with… · the same entry in another collection · chain E against E, 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 7NOV · PDBe 7NOV · UniProt P9WIT9
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