MolNFT v1 · #102319 · protein + DNA
Rage recognizes nucleic acids and promotes inflammatory responses to DNA
4OI7 · Advanced glycosylation end product-specific receptor: “Rage recognizes nucleic acids and promotes inflammatory responses to DNA”. X-ray diffraction, 5 pockets (best druggability 0.76). MolNFT v1 #102319 on GenesisL1: 3D structure…
- PDB
- 4OI7
- Type
- protein + DNA
- Length
- 470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Advanced glycosylation end product-specific receptor…
- UniProt
- Q15109
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Advanced glycosylation end product-specific receptor | protein | 211 | 3% helix, 49% strand | Q15109 |
| B | Advanced glycosylation end product-specific receptor | protein | 215 | 3% helix, 45% strand | Q15109 |
| E | 5'-D(*CP*TP*GP*CP*AP*AP*CP*GP*AP*TP*GP*CP*TP*AP*CP*GP*AP*AP *CP*GP*TP*G)-3' | dna | 22 | — | — |
| F | 5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*TP*AP*GP*CP*AP*TP*CP*GP*TP*TP *GP*CP*AP*G)-3' | dna | 22 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.76 | 0.82 | 60 | empty |
| 2 | 164 | 0.50 | 0.79 | 26 | empty |
| 3 | 125 | 0.48 | 0.78 | 26 | empty |
| 4 | 116 | 0.43 | 0.77 | 22 | EDO |
| 5 | 75 | 0.38 | 0.77 | 18 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1051 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- A–B · 564 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 236 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–E · 208 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 207 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4OI7 · RAGE recognizes nucleic acids and promotes inflammatory responses to DNA · the same entry in another collection · chain E against E, 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 4OI7 · PDBe 4OI7 · UniProt Q15109
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