MolNFT v1 · #92433 · protein
Crystal structure of voltage sensing domain of ci-vsp with fragment antibody (R217E, 2.8 a)
4G7Y · Fragment antibody heavy chain: “Crystal structure of voltage sensing domain of ci-vsp with fragment antibody (R217E, 2.8 a)”. X-ray diffraction, 2 ligands (MG, CL), 8 pockets (best druggability 0.70). MolNFT v1 #92433 on GenesisL1…
- PDB
- 4G7Y
- Type
- protein
- Length
- 554 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragment antibody heavy chain; Fragment antibody light chain; Voltage-sensor containing…
- UniProt
- Q4W8A1
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fragment antibody heavy chain | protein | 212 | 7% helix, 53% strand | — |
| L | Fragment antibody light chain | protein | 211 | 6% helix, 53% strand | — |
| S | Voltage-sensor containing phosphatase | protein | 131 | 77% helix, 0% strand | Q4W8A1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains L
- CL · Chloride ion · ion · chains L
- LDA · Lauryl dimethylamine-N-oxide · additive · chains L, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.70 | 0.95 | 17 | empty |
| 2 | 255 | 0.56 | 0.77 | 34 | LDA |
| 3 | 169 | 0.53 | 0.79 | 20 | empty |
| 4 | 64 | 0.53 | 0.87 | 19 | empty |
| 5 | 243 | 0.52 | 0.76 | 38 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1650 Ų buried · 11 hydrogen bonds · protein-protein
- L–S · 408 Ų buried · 6 hydrogen bonds · protein-protein
- H–S · 257 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4G7Y · Crystal structure of voltage sensing domain of Ci-VSP with fragment antibody (R217E, 2.8… · 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
- Every structure of UniProt Q4W8A1
- Elsewhere: RCSB PDB 4G7Y · PDBe 4G7Y · UniProt Q4W8A1
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