MolNFT v1 · #169894 · protein
Receptor for advanced glycation end products VC1 domain in complex with fragment 5
6XQ7 · Advanced glycosylation end product-specific receptor: “Receptor for advanced glycation end products VC1 domain in complex with fragment 5”. X-ray diffraction, 2 ligands (V6V, CL), 5 pockets (best druggability 0.43). MolNFT v1…
- PDB
- 6XQ7
- Type
- protein
- Length
- 424 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
- V6V, CL
- Pockets
- 5 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Advanced glycosylation end product-specific receptor | protein | 212 | 3% helix, 48% strand | Q15109 |
Ligands and binding sites
- V6V · 5-bromo-3-methyl-1H-indole-2-carboxylic acid · ligand · 7 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- ACT · Acetate ion · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.43 | 0.78 | 17 | empty |
| 2 | 129 | 0.40 | 0.75 | 21 | ACT, V6V |
| 3 | 92 | 0.39 | 0.76 | 21 | ACT |
| 4 | 53 | 0.32 | 0.77 | 16 | empty |
| 5 | 57 | 0.26 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6XQ7 · Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5 · 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 0.96
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 6XQ7 · PDBe 6XQ7 · UniProt Q15109
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