Research workbench
Dntr inducer binding domain in complex with salicylate. monoclinic crystal form
Analyse Dntr inducer binding domain in complex with salicylate. monoclinic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y7K
- Type
- protein
- Length
- 845 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
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysr-type regulatory protein | protein | 211 | 37% helix, 27% strand | Q7WT50 |
| B | Lysr-type regulatory protein | protein | 213 | 37% helix, 26% strand | Q7WT50 |
| C | Lysr-type regulatory protein | protein | 212 | 35% helix, 26% strand | Q7WT50 |
| D | Lysr-type regulatory protein | protein | 209 | 36% helix, 27% strand | Q7WT50 |
Ligands and binding sites
- SAL · 2-hydroxybenzoic acid · ligand · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.72 | 0.78 | 60 | empty |
| 2 | 61 | 0.71 | 0.97 | 21 | empty |
| 3 | 51 | 0.69 | 0.97 | 17 | SAL |
| 4 | 221 | 0.56 | 0.78 | 42 | empty |
| 5 | 58 | 0.45 | 0.83 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1476 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1377 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 750 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Y7K · DntR Inducer Binding Domain in Complex with Salicylate. Monoclinic crystal form · 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 2Y7K · PDBe 2Y7K · UniProt Q7WT50
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