Research workbench
Nanobody-anti-vglut nanobody complex
Analyse Nanobody-anti-vglut nanobody complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCL
- Type
- protein
- Length
- 959 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-llama nanobody; Anti-vglut nanobody
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Anti-llama nanobody | protein | 115 | 8% helix, 51% strand | — |
| B, G | Anti-vglut nanobody | protein | 127 | 7% helix, 50% strand | — |
| C | Anti-llama nanobody | protein | 117 | 5% helix, 47% strand | — |
| D | Anti-vglut nanobody | protein | 121 | 5% helix, 54% strand | — |
| E | Anti-vglut nanobody | protein | 119 | 5% helix, 55% strand | — |
| F | Anti-llama nanobody | protein | 118 | 3% helix, 50% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.54 | 0.76 | 31 | empty |
| 2 | 320 | 0.54 | 0.75 | 38 | empty |
| 3 | 143 | 0.50 | 0.79 | 38 | empty |
| 4 | 204 | 0.47 | 0.75 | 28 | empty |
| 5 | 93 | 0.41 | 0.78 | 21 | empty |
Interfaces
7 interfaces between chains.
- E–F · 694 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 687 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 662 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 640 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 635 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5OCL · Nanobody-anti-VGLUT nanobody complex · 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
- Elsewhere: RCSB PDB 5OCL · PDBe 5OCL
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