MolNFT v1 · #116045 · protein
Crystal structure of mycobacterium tuberculosis RV1816 transcriptional regulator.
5D1R: “Crystal structure of mycobacterium tuberculosis RV1816 transcriptional regulator.”. X-ray diffraction, 4 ligands (56S, NI, MG), 3 pockets (best druggability 0.82). MolNFT v1 #116045 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5D1R
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RV1816 transcriptional regulator
- UniProt
- P9WMC8
- Ligands
- 56S, NI, MG, SO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RV1816 transcriptional regulator | protein | 227 | 67% helix, 0% strand | P9WMC8 |
| B | RV1816 transcriptional regulator | protein | 226 | 69% helix, 0% strand | P9WMC8 |
Ligands and binding sites
- 56S · propan-2-yl dodecanoate · ligand · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.82 | 0.82 | 113 | 56S |
| 2 | 75 | 0.43 | 0.81 | 21 | SO4 |
| 3 | 53 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2152 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5D1R · Crystal structure of Mycobacterium tuberculosis Rv1816 transcriptional regulator. · the same entry in another collection · chain A against A, TM-score 1.00
- P9WMC8 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P9WMC8
- Elsewhere: RCSB PDB 5D1R · PDBe 5D1R · UniProt P9WMC8
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