Research workbench
The transcriptional regulator prfa from listeria monocytogenes in complex with inhibitor of wnt production (iwp)-2
Analyse The transcriptional regulator prfa from listeria monocytogenes in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T5I
- Type
- protein
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Listeriolysin positive regulatory factor a
- UniProt
- Q4TVQ0
- Ligands
- 9XK, NA
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Listeriolysin positive regulatory factor a | protein | 236 | 47% helix, 27% strand | Q4TVQ0 |
| B | Listeriolysin positive regulatory factor a | protein | 228 | 46% helix, 26% strand | Q4TVQ0 |
Ligands and binding sites
- 9XK · ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 11 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 | 470 | 0.77 | 0.85 | 53 | 9XK, DMS |
| 2 | 569 | 0.74 | 0.81 | 63 | DMS |
| 3 | 381 | 0.74 | 0.84 | 43 | DMS |
| 4 | 107 | 0.36 | 0.74 | 19 | DMS |
| 5 | 82 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2185 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6T5I · The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with inhibitor… · 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 Q4TVQ0
- Elsewhere: RCSB PDB 6T5I · PDBe 6T5I · UniProt Q4TVQ0
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