Research workbench
Crystal structure of mycobacterium tuberculosis argd with prosthetic group pyridoxal 5'-phosphate and 3-hydroxy-2-naphthoic acid.
Analyse Crystal structure of mycobacterium tuberculosis argd with prosthetic group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NN4
- Type
- protein
- Length
- 1,564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylornithine aminotransferase
- EC
- 2.6.1.11
- UniProt
- P9WPZ7
- Ligands
- BZJ, NO3
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acetylornithine aminotransferase (EC 2.6.1.11) | protein | 391 | 41% helix, 20% strand | P9WPZ7 |
Ligands and binding sites
- BZJ · 3-hydroxynaphthalene-2-carboxylic acid · ligand · 5 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.78 | 0.82 | 82 | empty |
| 2 | 50 | 0.71 | 0.99 | 18 | empty |
| 3 | 52 | 0.70 | 0.98 | 20 | empty |
| 4 | 361 | 0.69 | 0.82 | 41 | BZJ |
| 5 | 227 | 0.68 | 0.86 | 29 | BZJ, NO3 |
Interfaces
5 interfaces between chains.
- C–D · 4726 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 4720 Ų buried · 72 hydrogen bonds · protein-protein
- B–C · 192 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 115 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7NN4 · Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WPZ7 · AlphaFold monomer V2.0 prediction for acetylornithine aminotransferase (P9WPZ7) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P9WPZ7
- Elsewhere: RCSB PDB 7NN4 · PDBe 7NN4 · UniProt P9WPZ7
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