Research workbench
Structural and DNA binding studies of the transcriptional repressor RV2506 (bkar) from mycobacterium tuberculosis supports a role in L- leucine catabolism
Analyse Structural and DNA binding studies of the transcriptional repressor RV2506… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YJ2
- Type
- protein
- Length
- 755 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcriptional regulatory protein (probably tetr- family)
- UniProt
- O06169
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Probable transcriptional regulatory protein (probably tetr- family) | protein | 192 | 81% helix, 0% strand | O06169 |
| A | Probable transcriptional regulatory protein (probably tetr- family) | protein | 186 | 81% helix, 0% strand | O06169 |
| C | Probable transcriptional regulatory protein (probably tetr- family) | protein | 185 | 80% helix, 0% strand | O06169 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains B, D, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.82 | 0.83 | 79 | GOL |
| 2 | 1036 | 0.81 | 0.82 | 80 | GOL |
| 3 | 1036 | 0.74 | 0.77 | 83 | GOL |
| 4 | 115 | 0.47 | 0.79 | 18 | empty |
| 5 | 54 | 0.29 | 0.74 | 12 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1400 Ų buried · 6 hydrogen bonds · protein-protein
- D–C · 1389 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 567 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 79 Ų buried · 2 hydrogen bonds · protein-protein
- D–A · 42 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YJ2 · Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from… · the same entry in another collection · chain B against B, 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 O06169
- Elsewhere: RCSB PDB 6YJ2 · PDBe 6YJ2 · UniProt O06169
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