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Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann External Resource: Annotation Chains Domain Info Class Fold Superfamily Family Domain Species Provenance Source (Version) I d2ybri_ Small proteins Knottins (small inhibitors, toxins, lectins) Scorpion toxin-like Long-chain scorpion toxins Scorpion toxin Centruroides noxius ) [TaxId: 6878 ], SCOPe (2.08) F d2ybrf_ Small proteins Knottins (small inhibitors, toxins, lectins) Scorpion toxin-like Long-chain scorpion toxins Scorpion toxin Centruroides noxius ) [TaxId: 6878 ], SCOPe (2.08) C d2ybrc_ Small proteins Knottins (small inhibitors, toxins, lectins) Scorpion toxin-like Long-chain scorpion toxins Scorpion toxin Centruroides noxius ) [TaxId: 6878 ], SCOPe (2.08) H d2ybrh1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) H d2ybrh2 Artifacts Tags Tags Tags N-terminal Tags HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) E d2ybre1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) E d2ybre2 Artifacts Tags Tags Tags N-terminal Tags HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) B d2ybrb1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) B d2ybrb2 Artifacts Tags Tags Tags N-terminal Tags HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) G d2ybrg_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) automated matches HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) D d2ybrd_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) automated matches HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08) A d2ybra_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) automated matches HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Chains Type Family Name Domain Identifier Family Identifier Provenance Source (Version) I SCOP2B Superfamily Scorpion toxin-like 8038170 3000309 SCOP2B (2022-06-29) F SCOP2B Superfamily Scorpion toxin-like 8038170 3000309 SCOP2B (2022-06-29) C SCOP2B Superfamily Scorpion toxin-like 8038170 3000309 SCOP2B (2022-06-29)
Chains Family Name Domain Identifier Architecture Possible Homology Homology Topology Family Provenance Source (Version) I Globin e2ybrI1 A: alpha arrays X: Alpha-beta plaits H: Phage tail protein-like T: Transmembrane protein 14A F: Globin ECOD (v295.2) F Globin e2ybrF1 A: alpha arrays X: Alpha-beta plaits H: Phage tail protein-like T: Transmembrane protein 14A F: Globin ECOD (v295.2) C Globin e2ybrC1 A: alpha arrays X: Globin-like H: Globin-like T: Globin-like F: Globin ECOD (v295.2) H Globin e2ybrH1 A: alpha arrays X: Alpha-beta plaits H: Phage tail protein-like T: Transmembrane protein 14A F: Globin ECOD (v295.2) E Globin e2ybrE1 A: alpha arrays X: Alpha-beta plaits H: Phage tail protein-like T: Transmembrane protein 14A F: Globin ECOD (v295.2) B I-set e2ybrB1 A: alpha arrays X: Acyl-CoA binding protein-like H: Acyl-CoA binding protein-like T: Acyl-CoA binding protein-like F: I-set ECOD (v295.2) G Globin e2ybrG1 A: alpha arrays X: Alpha-beta plaits H: Phage tail protein-like T: Transmembrane protein 14A F: Globin ECOD (v295.2) D Globin e2ybrD1 A: alpha arrays X: Alpha-beta plaits H: Phage tail protein-like T: Transmembrane protein 14A F: Globin ECOD (v295.2) A Globin e2ybrA1 A: alpha arrays X: Globin-like H: Globin-like T: Globin-like F: Globin ECOD (v295.2)
Chain Protein Name Description Organism Name Gene Allele Name(s) Domain Name(s) Receptor Type Receptor Description Provenance Source 9004G, anti-Cn2 toxin V-KAPPA Homo sapiens (human) IGKV3D-11*01, IGKJ1*01 V-DOMAIN V-KAPPA IG SCFV-HEAVY-KAPPA IMGT (202637-0) 9004G, anti-Cn2 toxin VH Homo sapiens (human) IGHV3-9*01, IGHJ3*01, IGHJ3*02 V-DOMAIN VH IG SCFV-HEAVY-KAPPA IMGT (202637-0)
Chain Chain Class Chain Subclass Chain Type Antigen Name(s) Provenance Source Light Chain IGKV3 Kappa beta-mammal toxin cn2 SAbDab (2026-09-25) Heavy Chain IGHV3 - beta-mammal toxin cn2 SAbDab (2026-09-25)
Chains Polymer Molecular Function Biological Process Cellular Component BETA-MAMMAL TOXIN CN2 SINGLE CHAIN ANTIBODY FRAGMENT 9004G - - - SINGLE CHAIN ANTIBODY FRAGMENT 9004G - - -