Research workbench
Crystal structure of TLR13-SSRNA13 complex
Analyse Crystal structure of TLR13-SSRNA13 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z0C
- Type
- protein + RNA
- Length
- 1,444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 13; DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3')
- UniProt
- Q6R5N8
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Toll-like receptor 13 | protein | 709 | 10% helix, 18% strand | Q6R5N8 |
| B, C | DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3') | rna | 13 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.85 | 0.87 | 82 | empty |
| 2 | 389 | 0.62 | 0.77 | 40 | empty |
| 3 | 432 | 0.62 | 0.76 | 46 | empty |
| 4 | 218 | 0.51 | 0.77 | 23 | empty |
| 5 | 205 | 0.51 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- D–C · 1075 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1061 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–D · 1018 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–B · 459 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 24 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q6R5N8
- Elsewhere: RCSB PDB 4Z0C · PDBe 4Z0C · UniProt Q6R5N8
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