Research workbench
Crystal structure of monkey TLR7 in complex with gguccc
Analyse Crystal structure of monkey TLR7 in complex with gguccc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZSM
- Type
- protein + RNA
- Length
- 1,560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 7; RNA (5'-R(*GP*UP*CP*CP*C)-3')
- UniProt
- B3Y653
- Ligands
- 9K9, NAG, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Toll-like receptor 7 | protein | 776 | 13% helix, 15% strand | B3Y653 |
| A | Toll-like receptor 7 | protein | 774 | 12% helix, 15% strand | B3Y653 |
| D, E | RNA (5'-R(*GP*UP*CP*CP*C)-3') | rna | 5 | — | — |
Ligands and binding sites
- 9K9 · 2-amino-9-[(2s,3ar,4r,6r,6ar)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3, 4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one · ligand · 2 copies · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains B, A
- SO4 · Sulfate ion · ion · 9 copies · chains B, A, E, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.70 | 0.97 | 26 | SO4 |
| 2 | 536 | 0.68 | 0.78 | 57 | NAG |
| 3 | 158 | 0.67 | 0.87 | 37 | empty |
| 4 | 146 | 0.64 | 0.87 | 32 | empty |
| 5 | 229 | 0.62 | 0.82 | 38 | empty |
Interfaces
5 interfaces between chains.
- B–A · 2329 Ų buried · 40 hydrogen bonds · protein-protein
- B–E · 746 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 721 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 163 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–E · 160 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5ZSM · Crystal structure of monkey TLR7 in complex with GGUCCC · the same entry in another collection · chain B against B, 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 5ZSM · PDBe 5ZSM · UniProt B3Y653
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