Research workbench
Structure of reduced M smegmatis 5246, a homologue of M. tuberculosis acg
Analyse Structure of reduced M smegmatis 5246, a homologue of M. tuberculosis acg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YMV
- Type
- protein
- Length
- 327 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acg nitroreductase
- UniProt
- A0R2V4
- Ligands
- FNR
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acg nitroreductase | protein | 327 | 40% helix, 18% strand | A0R2V4 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · chains A
- FMT · Formic acid · additive · 3 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.82 | 0.94 | 46 | FNR |
| 2 | 109 | 0.41 | 0.77 | 18 | empty |
| 3 | 98 | 0.38 | 0.76 | 23 | empty |
| 4 | 55 | 0.36 | 0.79 | 16 | empty |
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2YMV · Structure of Reduced M Smegmatis 5246, a homologue of M.Tuberculosis Acg · the same entry in another collection · 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 A0R2V4
- Elsewhere: RCSB PDB 2YMV · PDBe 2YMV · UniProt A0R2V4
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