Research workbench
Crystal structure of monkey TLR7 in complex with guanosine and polyu
Analyse Crystal structure of monkey TLR7 in complex with guanosine and polyu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GMF
- Type
- protein + RNA
- Length
- 3,116 residues
- Chains
- 8
- 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
- GMP, NAG, CA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Toll-like receptor 7 | protein | 776 | 13% helix, 15% strand | B3Y653 |
| E, F, G, H | RNA (5'-R(P*UP*UP*UP*U)-3') | rna | 3 | — | — |
Ligands and binding sites
- GMP · Guanosine · ligand · 4 copies · chains B, D, A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.69 | 0.86 | 43 | empty |
| 2 | 583 | 0.68 | 0.78 | 60 | NAG |
| 3 | 232 | 0.68 | 0.85 | 40 | empty |
| 4 | 216 | 0.67 | 0.85 | 40 | empty |
| 5 | 398 | 0.67 | 0.80 | 55 | empty |
Interfaces
11 interfaces between chains.
- B–D · 2419 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2399 Ų buried · 44 hydrogen bonds · protein-protein
- B–F · 588 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–H · 584 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–G · 584 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 36 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 5GMF · Crystal structure of monkey TLR7 in complex with guanosine 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 5GMF · PDBe 5GMF · UniProt B3Y653
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