MolNFT v1 · #114413 · protein
Crystal structure of the artificial nanobody OCTARELLINV.1 complex
5BOP: “Crystal structure of the artificial nanobody OCTARELLINV.1 complex”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #114413 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BOP
- Type
- protein
- Length
- 575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody; Octarellin V.1
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nanobody | protein | 123 | 7% helix, 49% strand | — |
| B | Octarellin V.1 | protein | 167 | 45% helix, 19% strand | — |
| D | Octarellin V.1 | protein | 162 | 46% helix, 19% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.74 | 0.78 | 86 | empty |
| 2 | 85 | 0.45 | 0.80 | 22 | empty |
| 3 | 62 | 0.35 | 0.78 | 15 | empty |
| 4 | 69 | 0.32 | 0.75 | 17 | empty |
| 5 | 71 | 0.31 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 897 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 882 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 349 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 102 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5BOP · Crystal structure of the artificial nanobody octarellinV.1 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 5BOP · PDBe 5BOP
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