Research workbench
Crystal structure of a transcriptional regulator from oenococcus oeni
Analyse Crystal structure of a transcriptional regulator from oenococcus oeni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BY6
- Type
- protein
- Length
- 602 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted transcriptional regulator
- UniProt
- Q04D30
- Ligands
- CA
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted transcriptional regulator | protein | 119 | 61% helix, 8% strand | Q04D30 |
| B | Predicted transcriptional regulator | protein | 118 | 61% helix, 8% strand | Q04D30 |
| C | Predicted transcriptional regulator | protein | 120 | 60% helix, 8% strand | Q04D30 |
| D | Predicted transcriptional regulator | protein | 121 | 60% helix, 8% strand | Q04D30 |
| E | Predicted transcriptional regulator | protein | 124 | 60% helix, 8% strand | Q04D30 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.58 | 0.74 | 35 | empty |
| 2 | 56 | 0.40 | 0.81 | 12 | empty |
| 3 | 139 | 0.39 | 0.74 | 27 | empty |
| 4 | 77 | 0.34 | 0.75 | 18 | empty |
| 5 | 73 | 0.32 | 0.75 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1929 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 366 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 365 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 323 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 268 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3BY6 · Crystal structure of a transcriptional regulator from Oenococcus oeni · 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 Q04D30
- Elsewhere: RCSB PDB 3BY6 · PDBe 3BY6 · UniProt Q04D30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.