Research workbench
Structure of an RNA-binding light-oxygen-voltage receptor
Analyse Structure of an RNA-binding light-oxygen-voltage receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HMJ
- Type
- protein
- Length
- 1,419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative PAS/PAC sensor protein
- UniProt
- C8XJT7
- Ligands
- FMN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative PAS/PAC sensor protein | protein | 359 | 47% helix, 23% strand | C8XJT7 |
| B | Putative PAS/PAC sensor protein | protein | 352 | 44% helix, 23% strand | C8XJT7 |
| C | Putative PAS/PAC sensor protein | protein | 355 | 47% helix, 23% strand | C8XJT7 |
| D | Putative PAS/PAC sensor protein | protein | 353 | 44% helix, 23% strand | C8XJT7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
- IMD · Imidazole · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.76 | 0.91 | 24 | FMN |
| 2 | 191 | 0.75 | 0.91 | 25 | FMN |
| 3 | 185 | 0.74 | 0.90 | 25 | FMN |
| 4 | 166 | 0.74 | 0.91 | 25 | FMN |
| 5 | 546 | 0.69 | 0.79 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3491 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 3459 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 698 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 666 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6HMJ · Structure of an RNA-binding Light-Oxygen-Voltage Receptor · the same entry in another collection · chain D against D, 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 C8XJT7
- Elsewhere: RCSB PDB 6HMJ · PDBe 6HMJ · UniProt C8XJT7
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