Research workbench
Crystal structure of C-terminal domain of RV1828 from mycobacterium tuberculosis
Analyse Crystal structure of C-terminal domain of RV1828 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
- 5YDD
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized hth-type transcriptional regulator RV1828
- UniProt
- P9WME7
- Ligands
- 8TU, NA, SO4
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized hth-type transcriptional regulator RV1828 | protein | 120 | 71% helix, 2% strand | P9WME7 |
| B | Uncharacterized hth-type transcriptional regulator RV1828 | protein | 121 | 71% helix, 2% strand | P9WME7 |
Ligands and binding sites
- 8TU · (6R,8S,9S)-8-(hydroxymethyl)-6,11,11-tris(oxidanyl)-9-propyl-dodecanoic acid · ligand · chains A, B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.35 | 0.75 | 14 | 8TU |
| 2 | 87 | 0.33 | 0.74 | 13 | empty |
| 3 | 61 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2554 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YDD · Crystal structure of C-terminal domain of Rv1828 from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- P9WME7 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P9WME7
- Elsewhere: RCSB PDB 5YDD · PDBe 5YDD · UniProt P9WME7
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