MolNFT v1 · #170858 · protein + DNA
Structural and DNA binding studies of the transcriptional repressor RV2506 (bkar) from mycobacterium tuberculosis supports a role in L- leucine catabolism
6YL2 · Probable transcriptional regulatory protein (probably tetr…: “Structural and DNA binding studies of the transcriptional repressor RV2506 (bkar) from mycobacterium…”. X-ray diffraction, 7 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6YL2
- Type
- protein + DNA
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcriptional regulatory protein (probably tetr- family); DNA (5'…
- UniProt
- O06169
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Probable transcriptional regulatory protein (probably tetr- family) | protein | 192 | 79% helix, 0% strand | O06169 |
| G | DNA (5'- D(*AP*CP*GP*TP*TP*AP*AP*TP*GP*AP*CP*GP*AP*TP*TP*AP*AP*CP*CP*G)-3') | dna | 20 | — | — |
| H | DNA (5'- D(*CP*GP*GP*TP*TP*AP*AP*TP*CP*GP*TP*CP*AP*TP*TP*AP*AP*CP*GP*T)-3') | dna | 20 | — | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.81 | 0.83 | 85 | empty |
| 2 | 485 | 0.58 | 0.74 | 33 | empty |
| 3 | 115 | 0.45 | 0.78 | 21 | empty |
| 4 | 109 | 0.42 | 0.77 | 13 | empty |
| 5 | 89 | 0.41 | 0.78 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–A · 1426 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 875 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- B–G · 332 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–H · 329 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–H · 316 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6YL2 · 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 6YL2 · PDBe 6YL2 · UniProt O06169
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