MolNFT v1 · #120012 · protein + RNA
Crystal structure of monkey TLR7 in complex with loxoribine and polyu
5GMG · Toll-like receptor 7: “Crystal structure of monkey TLR7 in complex with loxoribine and polyu”. X-ray diffraction, 3 ligands (SDL, NAG, PO4), 17 pockets (best druggability 0.69). MolNFT v1 #120012 on GenesisL1: 3D structure, binding…
- PDB
- 5GMG
- Type
- protein + RNA
- Length
- 1,530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 7; RNA (5'-R(P*UP*UP*UP*U)-3')
- UniProt
- B3Y653
- Ligands
- SDL, NAG, PO4
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 7 | protein | 762 | 11% helix, 15% strand | B3Y653 |
| C, D | RNA (5'-R(P*UP*UP*UP*U)-3') | rna | 3 | — | — |
Ligands and binding sites
- SDL · 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.69 | 0.84 | 46 | empty |
| 2 | 235 | 0.65 | 0.83 | 47 | empty |
| 3 | 349 | 0.65 | 0.80 | 56 | empty |
| 4 | 273 | 0.64 | 0.81 | 36 | SDL |
| 5 | 378 | 0.64 | 0.79 | 64 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2415 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 580 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 574 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 77 Ų buried · 1 hydrogen bond · protein-nucleic
- A–D · 74 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5GMG · Crystal structure of monkey TLR7 in complex with loxoribine and polyU · the same entry in another collection · chain A against A, TM-score 1.00
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 B3Y653
- Elsewhere: RCSB PDB 5GMG · PDBe 5GMG · UniProt B3Y653
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