Research workbench
Crystal structure of mycobacterium tuberculosis argf in complex with 5-methyl-4-phenylthiazol-2-amine.
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
- 7NNZ
- Type
- protein
- Length
- 1,811 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
- PTZ, PO4
- Pockets
- 20 · 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 | 45% helix, 17% strand | P9WIT9 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 297 | 45% helix, 16% strand | P9WIT9 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 307 | 44% helix, 16% strand | P9WIT9 |
| D | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 298 | 46% helix, 16% strand | P9WIT9 |
| E | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 300 | 45% helix, 17% strand | P9WIT9 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 301 | 45% helix, 17% strand | P9WIT9 |
Ligands and binding sites
- PTZ · 5-methyl-4-phenyl-1,3-thiazol-2-amine · ligand · 5 copies · chains A, C, B, D, F, E
- PO4 · Phosphate ion · ion · 9 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.85 | 0.86 | 93 | empty |
| 2 | 564 | 0.78 | 0.85 | 54 | PTZ |
| 3 | 350 | 0.78 | 0.88 | 41 | empty |
| 4 | 180 | 0.76 | 0.92 | 37 | empty |
| 5 | 495 | 0.75 | 0.83 | 52 | PO4 |
Interfaces
10 interfaces between chains.
- B–C · 1112 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1042 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1040 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1033 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1031 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7NNZ · 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 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 7NNZ · PDBe 7NNZ · UniProt P9WIT9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.