MolNFT v1 · #139194 · protein
Crystal structure of mycobacterium tuberculosis marr family protein RV2887 complex with salicylic acid
5X80 · Uncharacterized hth-type transcriptional regulator RV2887: “Crystal structure of mycobacterium tuberculosis marr family protein RV2887 complex with salicylic acid”. X-ray diffraction, 2 ligands (SAL, SO4), 4 pockets (best…
- PDB
- 5X80
- Type
- protein
- Length
- 517 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized hth-type transcriptional regulator RV2887
- UniProt
- P9WME9
- Ligands
- SAL, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized hth-type transcriptional regulator RV2887 | protein | 137 | 66% helix, 4% strand | P9WME9 |
| B | Uncharacterized hth-type transcriptional regulator RV2887 | protein | 135 | 68% helix, 3% strand | P9WME9 |
| C | Uncharacterized hth-type transcriptional regulator RV2887 | protein | 122 | 76% helix, 3% strand | P9WME9 |
| D | Uncharacterized hth-type transcriptional regulator RV2887 | protein | 123 | 75% helix, 3% strand | P9WME9 |
Ligands and binding sites
- SAL · 2-hydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.78 | 0.86 | 51 | SAL |
| 2 | 418 | 0.77 | 0.86 | 54 | SAL |
| 3 | 164 | 0.44 | 0.74 | 25 | empty |
| 4 | 102 | 0.43 | 0.78 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2140 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1958 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 407 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X80 · Crystal structure of mycobacterium tuberculosis marr family protein RV2887 complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WME9 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor RV2887 (P9WME9) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 P9WME9
- Elsewhere: RCSB PDB 5X80 · PDBe 5X80 · UniProt P9WME9
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