MolNFT v1 · #98957 · protein
Crystal structure of the human rage VC1 fragment in space group P62
4LP4 · Advanced glycosylation end product-specific receptor: “Crystal structure of the human rage VC1 fragment in space group P62”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.45). MolNFT v1 #98957 on GenesisL1: 3D…
- 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
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