Research workbench
Caffeine recognizing nanobody
Analyse Caffeine recognizing nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTL
- Type
- protein
- Length
- 948 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vhh
- Ligands
- CFF
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Vhh | protein | 117 | 5% helix, 56% strand | — |
| A | Vhh | protein | 119 | 8% helix, 55% strand | — |
| B, C, F, G | Vhh | protein | 119 | 5% helix, 55% strand | — |
| D, E | Vhh | protein | 118 | 5% helix, 55% strand | — |
Ligands and binding sites
- CFF · Caffeine · ligand · 4 copies · chains H, B, A, C, F, D, G, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.77 | 0.94 | 28 | CFF |
| 2 | 138 | 0.75 | 0.93 | 32 | CFF |
| 3 | 154 | 0.74 | 0.91 | 29 | CFF |
| 4 | 533 | 0.70 | 0.79 | 50 | CFF |
| 5 | 416 | 0.56 | 0.74 | 40 | empty |
Interfaces
12 interfaces between chains.
- A–C · 973 Ų buried · 13 hydrogen bonds · protein-protein
- H–B · 959 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 956 Ų buried · 8 hydrogen bonds · protein-protein
- D–G · 942 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 438 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6QTL · Caffeine recognizing nanobody · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 6QTL · PDBe 6QTL
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