Research workbench
Structure of RV3853 from mycobacterium tuberculosis
Analyse Structure of RV3853 from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NXJ
- Type
- protein
- Length
- 465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable S-ADENOSYLMETHIONINE:2- demethylmenaquinone methyltransferase
- EC
- 2.1.-.-
- UniProt
- P0A666
- Ligands
- GLV
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable S-ADENOSYLMETHIONINE:2- demethylmenaquinone methyltransferase (EC 2.1.-.-) | protein | 156 | 19% helix, 35% strand | P0A666 |
| B | Probable S-ADENOSYLMETHIONINE:2- demethylmenaquinone methyltransferase (EC 2.1.-.-) | protein | 155 | 18% helix, 35% strand | P0A666 |
| C | Probable S-ADENOSYLMETHIONINE:2- demethylmenaquinone methyltransferase (EC 2.1.-.-) | protein | 154 | 18% helix, 36% strand | P0A666 |
Ligands and binding sites
- GLV · Glyoxylic acid · ligand · 3 copies · chains A, B, C
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.56 | 0.77 | 35 | empty |
| 2 | 65 | 0.38 | 0.79 | 15 | TLA |
Interfaces
1 interface between chains.
- A–C · 449 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1NXJ · Structure of Rv3853 from Mycobacterium tuberculosis · 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 P0A666
- Elsewhere: RCSB PDB 1NXJ · PDBe 1NXJ · UniProt P0A666
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