MolNFT v1 · #55052 · protein
Dntr inducer binding domain
2Y84 · Lysr-type regulatory protein: “Dntr inducer binding domain”. X-ray diffraction, 17 pockets (best druggability 0.74). MolNFT v1 #55052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y84
- Type
- protein
- Length
- 1,701 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr-type regulatory protein
- UniProt
- Q7WT50
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysr-type regulatory protein | protein | 213 | 31% helix, 27% strand | Q7WT50 |
| B, C, G | Lysr-type regulatory protein | protein | 213 | 34% helix, 28% strand | Q7WT50 |
| D, E | Lysr-type regulatory protein | protein | 212 | 33% helix, 27% strand | Q7WT50 |
| F | Lysr-type regulatory protein | protein | 214 | 32% helix, 27% strand | Q7WT50 |
| H | Lysr-type regulatory protein | protein | 211 | 33% helix, 28% strand | Q7WT50 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains D, B, A, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.74 | 0.83 | 67 | empty |
| 2 | 538 | 0.73 | 0.81 | 58 | empty |
| 3 | 490 | 0.71 | 0.81 | 60 | empty |
| 4 | 373 | 0.70 | 0.82 | 72 | empty |
| 5 | 352 | 0.69 | 0.82 | 64 | empty |
Interfaces
11 interfaces between chains.
- F–G · 1544 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1513 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 1513 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1478 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2Y84 · 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 2Y84 · PDBe 2Y84 · UniProt Q7WT50
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