2YBR: Single chain antibody fragment 9004G
Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann. Determined by X-ray diffraction at 2.55 Å resolution. Released 13 Apr 2011.
- Method
- X-ray diffraction
- Resolution
- 2.55 Å
- Organisms
- HOMO SAPIENS, CENTRUROIDES NOXIUS HOFFMANN
- Chains
- 9
- Atoms
- 6,941
- Mol. weight
- 106.68 kDa
- Released
- 13 Apr 2011
Explore 2YBR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2YBR contains 25 α-helices and 92 β-strands across 9 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 4 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 1 |
| β-strand | 10-12 | 3 | 2 |
| β-strand | 18-25 | 8 | 1 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 2 |
| β-strand | 45-51 | 7 | 2 |
| α-helix | 53-55 | 3 | |
| β-strand | 58-60 | 3 | 2 |
| α-helix | 62-64 | 3 | |
| β-strand | 65 | 1 | 1 |
| β-strand | 68-73 | 6 | 1 |
| β-strand | 78-83 | 6 | 1 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-101 | 10 | 2 |
| β-strand | 103-107 | 5 | 2 |
| β-strand | 111-115 | 5 | 2 |
Chain B: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 136-139 | 4 | 3 |
| β-strand | 142-145 | 4 | 4 |
| β-strand | 151-157 | 7 | 3 |
| β-strand | 165-170 | 6 | 4 |
| β-strand | 177-180 | 4 | 4 |
| β-strand | 186 | 1 | 4 |
| α-helix | 187 | 1 | |
| β-strand | 194-198 | 5 | 3 |
| β-strand | 202-207 | 6 | 3 |
| α-helix | 212-214 | 3 | |
| β-strand | 217-222 | 6 | 4 |
| β-strand | 229-230 | 2 | 4 |
| β-strand | 234-238 | 5 | 4 |
Chains C and F: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 5 |
| β-strand | 6 | 1 | 6 |
| β-strand | 13 | 1 | 6 |
| β-strand | 15 | 1 | 5 |
| β-strand | 20 | 1 | 5 |
| α-helix | 23-33 | 11 | |
| β-strand | 38-42 | 5 | 5 |
| β-strand | 45-49 | 5 | 5 |
| α-helix | 59-60 | 2 | |
Chains D and G: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 7 |
| β-strand | 11 | 1 | 8 |
| β-strand | 18-25 | 8 | 7 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 9 |
| β-strand | 45-51 | 7 | 9 |
| α-helix | 53-55 | 3 | |
| β-strand | 58-60 | 3 | 9 |
| α-helix | 62-64 | 3 | |
| β-strand | 65 | 1 | 7 |
| β-strand | 68-73 | 6 | 7 |
| β-strand | 78-83 | 6 | 7 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-100 | 9 | 9 |
| β-strand | 103-107 | 5 | 9 |
| β-strand | 111-113 | 3 | 9 |
| β-strand | 114 | 1 | 8 |
Chain E: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 136-139 | 4 | 10 |
| β-strand | 142-144 | 3 | 11 |
| β-strand | 151-157 | 7 | 10 |
| β-strand | 165-170 | 6 | 11 |
| β-strand | 177-180 | 4 | 11 |
| β-strand | 186 | 1 | 11 |
| α-helix | 187 | 1 | |
| β-strand | 194-198 | 5 | 10 |
| β-strand | 202-207 | 6 | 10 |
| α-helix | 212-214 | 3 | |
| β-strand | 217-222 | 6 | 11 |
| β-strand | 229-230 | 2 | 11 |
| β-strand | 234-237 | 4 | 11 |
Chain H: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 136-139 | 4 | 17 |
| β-strand | 142-145 | 4 | 18 |
| β-strand | 151-157 | 7 | 17 |
| β-strand | 165-170 | 6 | 18 |
| α-helix | 175-176 | 2 | |
| β-strand | 177-182 | 6 | 18 |
| β-strand | 185-186 | 2 | 18 |
| α-helix | 187 | 1 | |
| β-strand | 194-199 | 6 | 17 |
| β-strand | 202-207 | 6 | 17 |
| α-helix | 212-214 | 3 | |
| β-strand | 217-222 | 6 | 18 |
| α-helix | 228 | 1 | |
| β-strand | 229-230 | 2 | 18 |
| β-strand | 234-238 | 5 | 18 |
Chain I: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 19 |
| β-strand | 6 | 1 | 20 |
| β-strand | 13 | 1 | 20 |
| β-strand | 15 | 1 | 19 |
| β-strand | 20 | 1 | 19 |
| α-helix | 23-33 | 11 | |
| β-strand | 38-42 | 5 | 19 |
| β-strand | 45-49 | 5 | 19 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Single chain antibody fragment 9004G | A, D, G | protein | 117 | HOMO SAPIENS | |
| Single chain antibody fragment 9004G | B, E, H | protein | 146 | HOMO SAPIENS | |
| Beta-mammal toxin CN2 | C, F, I | protein | 66 | CENTRUROIDES NOXIUS HOFFMANN | P01495 (AlphaFold model) |
Sequence of entity 1 (A, D, G), FASTA
>2YBR_1 SINGLE CHAIN ANTIBODY FRAGMENT 9004G (chains A, D, G)
EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDY
ADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTVSS
Sequence of entity 2 (B, E, H), FASTA
>2YBR_2 SINGLE CHAIN ANTIBODY FRAGMENT 9004G (chains B, E, H)
GGGGSGGGGSGGGGSEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPR
LLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVE
IKRAAAEQKLISEEDLNGAAHHHHHH
Sequence of entity 3 (C, F, I), FASTA
>2YBR_3 BETA-MAMMAL TOXIN CN2 (chains C, F, I)
KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPL
PNKRCS
Primary citation
Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides Noxius Hoffmann by a Human-Derived Single Chain Antibody Fragment. Canul-Tec, J.C., Riano-Umbarila, L., Rudino-Pinera, E. et al. J Biol Chem (2011) 286:20892. DOI 10.1074/JBC.M111.238410 · PubMed
Other PDB entries of the same protein (UniProt P01495 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2YC1 1.9 Å, Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in…
- 25IH 2.8 Å, Cryo-EM structure of human Nav1.6 in complex with Cn2
- 4V1D 3.1 Å, Ternary complex among two human derived single chain antibody fragments and Cn2 toxin…
- 1CN2 Solution structure of toxin 2 from centruroides noxius hoffmann, a beta scorpion…
Browse structure collections
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