Research workbench
Receptor for advanced glycation end products VC1 domain in complex with 3-(3-(((3-(4-CARBOXYPHENOXY)BENZYL)OXY)METHYL)PHENYL)-1H-indole- 2-carboxylic acid
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
- 6XQ3
- 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
- V6Y, CL
- Pockets
- 5 · best druggability 0.39
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
- V6Y · 3-(3-{[3-(4-carboxyphenoxy)phenyl]methoxy}phenyl)-1H-indole-2-carboxylic acid · ligand · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 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 | 120 | 0.39 | 0.74 | 18 | V6Y |
| 2 | 75 | 0.37 | 0.77 | 17 | empty |
| 3 | 62 | 0.37 | 0.78 | 18 | empty |
| 4 | 60 | 0.31 | 0.76 | 15 | empty |
| 5 | 56 | 0.25 | 0.72 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 512 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6XQ3 · Receptor for Advanced Glycation End Products VC1 domain in complex with… · 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 6XQ3 · PDBe 6XQ3 · UniProt Q15109
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