Research workbench
Crystal structure of the human derived single chain antibody fragment (scfv) 9004G in complex with CN2 toxin from the scorpion centruroides noxius hoffmann
Analyse Crystal structure of the human derived single chain antibody fragment (scfv)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YC1
- Type
- protein
- Length
- 580 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single chain antibody fragment 9004G; Beta-mammal toxin CN2
- UniProt
- P01495
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Single chain antibody fragment 9004G | protein | 117 | 10% helix, 54% strand | — |
| B, E | Single chain antibody fragment 9004G | protein | 108 | 3% helix, 49% strand | — |
| C, F | Beta-mammal toxin CN2 | protein | 65 | 17% helix, 25% strand | P01495 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, D, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.63 | 0.77 | 50 | empty |
| 2 | 435 | 0.62 | 0.77 | 53 | empty |
| 3 | 201 | 0.56 | 0.79 | 37 | empty |
| 4 | 130 | 0.42 | 0.76 | 24 | GOL |
| 5 | 135 | 0.40 | 0.74 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–C · 643 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 642 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 637 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 633 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 490 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2YC1 · Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in… · the same entry in another collection · chain C against C, TM-score 1.00
- P01495 · AlphaFold monomer V2.0 prediction for beta-mammal toxin CN2 (P01495) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P01495
- Elsewhere: RCSB PDB 2YC1 · PDBe 2YC1 · UniProt P01495
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