MolNFT v1 · #174195 · protein
Llama nanobody NB18 raised against gldl from flavobacterium jonhsoniae
7BNW: “Llama nanobody NB18 raised against gldl from flavobacterium jonhsoniae”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #174195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BNW
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB18
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nanobody NB18 | protein | 120 | 3% helix, 57% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.63 | 0.76 | 53 | empty |
| 2 | 70 | 0.53 | 0.86 | 23 | empty |
| 3 | 144 | 0.41 | 0.74 | 28 | empty |
| 4 | 53 | 0.26 | 0.73 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–C · 494 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 454 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7BNW · Llama nanobody nb18 raised against GldL from Flavobacterium jonhsoniae · 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 7BNW · PDBe 7BNW
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