MolNFT v1 · #186210 · protein
NB82, a nanobody against voltage gated sodium channels NAV1.4 and NAV1.5
7R63 · Nanobody NB82: “NB82, a nanobody against voltage gated sodium channels NAV1.4 and NAV1.5”. X-ray diffraction, 3 ligands (NA, SO4, CL), 3 pockets (best druggability 0.84). MolNFT v1 #186210 on GenesisL1: 3D structure, binding sites…
- PDB
- 7R63
- Type
- protein
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB82
- Ligands
- NA, SO4, CL
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody NB82 | protein | 128 | 7% helix, 51% strand | — |
| B | Nanobody NB82 | protein | 125 | 7% helix, 51% strand | — |
| C, D | Nanobody NB82 | protein | 130 | 9% helix, 49% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, D, C, B
- CL · Chloride ion · ion · chains C
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.84 | 0.85 | 101 | SO4 |
| 2 | 87 | 0.33 | 0.74 | 19 | empty |
| 3 | 87 | 0.32 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 656 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 503 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 211 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 151 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7R63 · Nb82, a nanobody against voltage gated sodium channels Nav1.4 and Nav1.5 · 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 7R63 · PDBe 7R63
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