Research workbench
Lyttr DNA-binding domain of putative methyl-ACCEPTING/DNA response regulator from bacillus cereus.
Analyse Lyttr DNA-binding domain of putative methyl-ACCEPTING/DNA response regulator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D6W
- Type
- protein
- Length
- 218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-ACCEPTING/DNA response regulator
- UniProt
- Q73A38
- Ligands
- MG
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-ACCEPTING/DNA response regulator | protein | 109 | 19% helix, 46% strand | Q73A38 |
| B | Methyl-ACCEPTING/DNA response regulator | protein | 109 | 19% helix, 50% strand | Q73A38 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.63 | 0.85 | 28 | empty |
| 2 | 53 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 626 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3D6W · LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from… · 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 Q73A38
- Elsewhere: RCSB PDB 3D6W · PDBe 3D6W · UniProt Q73A38
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