MolNFT v1 · #34144 · protein
Crystal structure of transcriptional factor SCO4008 from streptomyces coelicolor A3(2)
2D6Y · Putative tetr family regulatory protein: “Crystal structure of transcriptional factor SCO4008 from streptomyces coelicolor A3(2)”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #34144 on GenesisL1: 3D structure…
- PDB
- 2D6Y
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative tetr family regulatory protein
- UniProt
- Q9ADP7
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative tetr family regulatory protein | protein | 186 | 78% helix, 0% strand | Q9ADP7 |
| B | Putative tetr family regulatory protein | protein | 188 | 77% helix, 0% strand | Q9ADP7 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.72 | 0.97 | 18 | TLA |
| 2 | 506 | 0.71 | 0.80 | 61 | empty |
| 3 | 90 | 0.62 | 0.88 | 21 | TLA |
| 4 | 73 | 0.34 | 0.76 | 18 | empty |
| 5 | 52 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2405 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2D6Y · Crystal Structure of transcriptional factor SCO4008 from Streptomyces coelicolor A3(2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ADP7 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor SCO4008 (Q9ADP7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9ADP7
- Elsewhere: RCSB PDB 2D6Y · PDBe 2D6Y · UniProt Q9ADP7
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