MolNFT v1 · #55162 · protein
Crystal structure of the human derived single chain antibody fragment (scfv) 9004G in complex with CN2 toxin from the scorpion centruroides noxius hoffmann
2YBR · Single chain antibody fragment 9004G: “Crystal structure of the human derived single chain antibody fragment (scfv) 9004G in complex with CN2 toxin…”. X-ray diffraction, 8 pockets (best druggability 0.76). MolNFT v1 #55162 on…
- PDB
- 2YBR
- Type
- protein
- Length
- 875 residues
- Chains
- 9
- 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
- 8 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single chain antibody fragment 9004G | protein | 116 | 10% helix, 55% strand | — |
| B | Single chain antibody fragment 9004G | protein | 112 | 3% helix, 45% strand | — |
| C, F | Beta-mammal toxin CN2 | protein | 65 | 17% helix, 25% strand | P01495 |
| D, G | Single chain antibody fragment 9004G | protein | 115 | 10% helix, 53% strand | — |
| E | Single chain antibody fragment 9004G | protein | 107 | 3% helix, 45% strand | — |
| H | Single chain antibody fragment 9004G | protein | 114 | 3% helix, 47% strand | — |
| I | Beta-mammal toxin CN2 | protein | 66 | 17% helix, 24% strand | P01495 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.76 | 0.79 | 118 | empty |
| 2 | 393 | 0.62 | 0.77 | 48 | empty |
| 3 | 239 | 0.59 | 0.80 | 31 | empty |
| 4 | 133 | 0.43 | 0.76 | 24 | empty |
| 5 | 131 | 0.41 | 0.75 | 27 | empty |
Interfaces
12 interfaces between chains.
- A–B · 695 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 694 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 690 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 647 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 642 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 2YBR · Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in… · the same entry in another collection · chain I against I, 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 0.96
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 2YBR · PDBe 2YBR · UniProt P01495
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