Research workbench
Crystal structure of mycobacterium tuberculosis argf in complex with methyl 4-hydroxy-3-iodobenzoate.
Analyse Crystal structure of mycobacterium tuberculosis argf in complex with methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NNW
- Type
- protein
- Length
- 1,805 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
- 98T, PO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 308 | 44% 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 | 45% helix, 16% 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 | 299 | 45% helix, 17% strand | P9WIT9 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 299 | 46% helix, 17% strand | P9WIT9 |
Ligands and binding sites
- 98T · methyl 3-iodanyl-4-oxidanyl-benzoate · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.85 | 0.87 | 64 | empty |
| 2 | 752 | 0.80 | 0.84 | 83 | 98T |
| 3 | 772 | 0.80 | 0.84 | 91 | 98T |
| 4 | 505 | 0.77 | 0.85 | 56 | 98T |
| 5 | 402 | 0.75 | 0.85 | 49 | 98T |
Interfaces
10 interfaces between chains.
- B–C · 1039 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1035 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1021 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1020 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1008 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7NNW · Crystal structure of Mycobacterium tuberculosis ArgF in complex with methyl… · 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 C 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 7NNW · PDBe 7NNW · UniProt P9WIT9
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