MolNFT v1 · #114948 · protein
Crystal structure of putative tetr family transcription factor from listeria monocytogenes
5C4Y · Putative transcription regulator LMO0852: “Crystal structure of putative tetr family transcription factor from listeria monocytogenes”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #114948 on GenesisL1: 3D…
- PDB
- 5C4Y
- Type
- protein
- Length
- 272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transcription regulator LMO0852
- UniProt
- Q8Y8P4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative transcription regulator LMO0852 | protein | 136 | 82% helix, 0% strand | Q8Y8P4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.75 | 0.94 | 24 | empty |
| 2 | 155 | 0.66 | 0.87 | 35 | empty |
| 3 | 70 | 0.42 | 0.80 | 14 | empty |
| 4 | 75 | 0.36 | 0.76 | 12 | empty |
| 5 | 50 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1260 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5C4Y · Crystal structure of putative TetR family transcription factor from Listeria monocytogenes · 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 Q8Y8P4
- Elsewhere: RCSB PDB 5C4Y · PDBe 5C4Y · UniProt Q8Y8P4
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