Research workbench
Crystal structure of the human rage VC1 fragment in space group P62
Analyse Crystal structure of the human rage VC1 fragment in space group P62 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LP4
- 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
- NA
- Pockets
- 7 · best druggability 0.45
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
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.45 | 0.78 | 19 | empty |
| 2 | 102 | 0.43 | 0.78 | 19 | empty |
| 3 | 138 | 0.40 | 0.74 | 23 | empty |
| 4 | 151 | 0.39 | 0.73 | 25 | empty |
| 5 | 86 | 0.32 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4LP4 · Crystal structure of the human RAGE VC1 fragment in space group P62 · 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 4LP4 · PDBe 4LP4 · UniProt Q15109
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.