Research workbench
Dntr inducer binding domain
Analyse Dntr inducer binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y7W
- Type
- protein
- Length
- 831 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr-type regulatory protein
- UniProt
- Q7WT50
- Ligands
- SAL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysr-type regulatory protein | protein | 207 | 34% helix, 29% strand | Q7WT50 |
| B | Lysr-type regulatory protein | protein | 207 | 33% helix, 29% strand | Q7WT50 |
| C | Lysr-type regulatory protein | protein | 207 | 34% helix, 29% strand | Q7WT50 |
| D | Lysr-type regulatory protein | protein | 210 | 30% helix, 28% strand | Q7WT50 |
Ligands and binding sites
- SAL · 2-hydroxybenzoic acid · ligand · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.80 | 0.83 | 108 | SAL |
| 2 | 623 | 0.76 | 0.82 | 77 | SAL, PG4 |
| 3 | 72 | 0.73 | 0.96 | 20 | empty |
| 4 | 115 | 0.65 | 0.88 | 28 | empty |
| 5 | 107 | 0.52 | 0.82 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1505 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1419 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Y7W · DntR Inducer Binding Domain · 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 Q7WT50
- Elsewhere: RCSB PDB 2Y7W · PDBe 2Y7W · UniProt Q7WT50
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