Research workbench
Crystal structure of ADP-bound bacterial GET3-like a and B in mycobacterium tuberculosis
Analyse Crystal structure of ADP-bound bacterial GET3-like a and B in mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BS3
- Type
- protein
- Length
- 685 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ATPase RV3679; Anion transporter
- UniProt
- P9WKX5, A0A089QYG8
- Ligands
- ADP, MG, CA
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ATPase RV3679 | protein | 330 | 51% helix, 16% strand | P9WKX5 |
| B | Anion transporter | protein | 355 | 57% helix, 14% strand | A0A089QYG8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains B
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.82 | 0.84 | 90 | ADP, MG |
| 2 | 156 | 0.60 | 0.83 | 20 | empty |
| 3 | 68 | 0.48 | 0.84 | 19 | empty |
| 4 | 78 | 0.47 | 0.82 | 14 | empty |
| 5 | 53 | 0.44 | 0.83 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2313 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6BS3 · Crystal structure of ADP-bound bacterial Get3-like A and B in Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- P9WKX5 · AlphaFold monomer V2.0 prediction for putative ATPase RV3679 (P9WKX5) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P9WKX5
- Every structure of UniProt A0A089QYG8
- Elsewhere: RCSB PDB 6BS3 · PDBe 6BS3 · UniProt P9WKX5 · UniProt A0A089QYG8
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