MolNFT v1 · #92430 · protein
Crystal structure of voltage sensing domain of ci-vsp with fragment antibody (R217E, 2.5 a)
4G7V · Fragment antibody heavy chain: “Crystal structure of voltage sensing domain of ci-vsp with fragment antibody (R217E, 2.5 a)”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.67). MolNFT v1 #92430 on GenesisL1: 3D…
- PDB
- 4G7V
- Type
- protein
- Length
- 562 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
- CL
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fragment antibody heavy chain | protein | 215 | 8% helix, 53% strand | — |
| L | Fragment antibody light chain | protein | 211 | 5% helix, 52% strand | — |
| S | Voltage-sensor containing phosphatase | protein | 136 | 79% helix, 0% strand | Q4W8A1 |
Ligands and binding sites
- CL · Chloride ion · ion · chains L
- LDA · Lauryl dimethylamine-N-oxide · additive · 3 copies · chains H, S, L
- SIN · Succinic acid · additive · chains L, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.67 | 0.95 | 16 | empty |
| 2 | 386 | 0.64 | 0.78 | 51 | LDA |
| 3 | 540 | 0.59 | 0.73 | 58 | empty |
| 4 | 184 | 0.56 | 0.80 | 22 | empty |
| 5 | 90 | 0.32 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1620 Ų buried · 15 hydrogen bonds · protein-protein
- L–S · 437 Ų buried · 6 hydrogen bonds · protein-protein
- H–S · 256 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4G7V · Crystal structure of voltage sensing domain of Ci-VSP with fragment antibody (R217E, 2.5… · 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 4G7V · PDBe 4G7V · UniProt Q4W8A1
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