Research workbench
Receptor for advanced glycation end products VC1 domain in complex with fragments 1 & 11
Analyse Receptor for advanced glycation end products VC1 domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XQ8
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Advanced glycosylation end product-specific receptor
- UniProt
- Q15109
- Ligands
- V6P, V6M, CL
- Pockets
- 6 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Advanced glycosylation end product-specific receptor | protein | 205 | 3% helix, 50% strand | Q15109 |
| B | Advanced glycosylation end product-specific receptor | protein | 206 | 3% helix, 50% strand | Q15109 |
Ligands and binding sites
- V6P · 3-phenoxyphenol · ligand · 3 copies · chains A, B
- V6M · 7-methyl-3-phenyl-1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- ACT · Acetate ion · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.47 | 0.77 | 20 | V6P |
| 2 | 81 | 0.38 | 0.77 | 17 | empty |
| 3 | 62 | 0.34 | 0.76 | 15 | empty |
| 4 | 75 | 0.29 | 0.72 | 23 | empty |
| 5 | 77 | 0.29 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 464 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6XQ8 · Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11 · the same entry in another collection · chain A against A, TM-score 1.00
- Q15109 · AlphaFold monomer V2.0 prediction for advanced glycosylation end product-specific… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q15109
- Elsewhere: RCSB PDB 6XQ8 · PDBe 6XQ8 · UniProt Q15109
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.