MolNFT v1 · #116050 · protein
Crystal structure of mycobacterium tuberculosis RV3249C transcriptional regulator.
5D1W: “Crystal structure of mycobacterium tuberculosis RV3249C transcriptional regulator.”. X-ray diffraction, 1 ligand (PLM), 20 pockets (best druggability 0.86). MolNFT v1 #116050 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5D1W
- Type
- protein
- Length
- 1,162 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RV3249C transcriptional regulator
- UniProt
- O05892
- Ligands
- PLM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RV3249C transcriptional regulator | protein | 195 | 72% helix, 0% strand | O05892 |
| C | RV3249C transcriptional regulator | protein | 192 | 72% helix, 0% strand | O05892 |
| D | RV3249C transcriptional regulator | protein | 196 | 72% helix, 2% strand | O05892 |
| E | RV3249C transcriptional regulator | protein | 193 | 70% helix, 0% strand | O05892 |
| F | RV3249C transcriptional regulator | protein | 191 | 74% helix, 1% strand | O05892 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.86 | 0.96 | 40 | PLM |
| 2 | 279 | 0.85 | 0.95 | 36 | PLM |
| 3 | 322 | 0.84 | 0.94 | 43 | empty |
| 4 | 240 | 0.84 | 0.95 | 35 | PLM |
| 5 | 408 | 0.83 | 0.91 | 53 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1688 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1623 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1604 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 264 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 261 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5D1W · Crystal structure of Mycobacterium tuberculosis Rv3249c transcriptional regulator. · 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 O05892
- Elsewhere: RCSB PDB 5D1W · PDBe 5D1W · UniProt O05892
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