2YC1
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
- Domain Annotation: SCOP/SCOPe Classification
- Domain Annotation: SCOP2 Classification
- Domain Annotation: ECOD Classification
- Domain Annotation: CATH
- IMGT Antibody Annotation
- SAbDab Antibody Annotation
- Protein Family Annotation
- Gene Ontology: Gene Product Annotation
- InterPro: Protein Family Classification
- Membrane Protein Annotation: OPM
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | V-set_12 | e2yc1A1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
D | V-set_12 | e2yc1D1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
B | V-set | e2yc1B1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (1.6) |
E | V-set | e2yc1E1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (1.6) |
C | Toxin_3 | e2yc1C1 | A: few secondary structure elements | X: omega toxin-like | H: omega toxin-related | T: Scorpion toxin-like | F: Toxin_3 | ECOD (1.6) |
F | Toxin_3 | e2yc1F1 | A: few secondary structure elements | X: omega toxin-like | H: omega toxin-related | T: Scorpion toxin-like | F: Toxin_3 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
D | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
B | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
E | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
C | 3.30.30.10 | Alpha Beta | 2-Layer Sandwich | Defensin A-like | Knottin, scorpion toxin-like | CATH (4.3.0) |
F | 3.30.30.10 | Alpha Beta | 2-Layer Sandwich | Defensin A-like | Knottin, scorpion toxin-like | CATH (4.3.0) |
IMGT Antibody Annotation IMGT Database Homepage
Chain | Protein Name | Description | Organism Name | Gene Allele Name(s) | Domain Name(s) | Receptor Type | Receptor Description | Provenance Source |
---|---|---|---|---|---|---|---|---|
9004G, anti-Cn2 toxin | VH | Homo sapiens (human) | IGHV3-9*01, IGHJ3*01 | V-DOMAIN VH | IG | SCFV-HEAVY-KAPPA | IMGT (202433-0) | |
9004G, anti-Cn2 toxin | V-KAPPA | Homo sapiens (human) | IGKV3D-11*02, IGKJ1*01 | V-DOMAIN V-KAPPA | IG | SCFV-HEAVY-KAPPA | IMGT (202433-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
Heavy Chain | IGHV3 | - | beta-mammal toxin cn2 | SAbDab (2024-08-23) | |
Light Chain | IGKV3 | Kappa | beta-mammal toxin cn2 | SAbDab (2024-08-23) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00537 | Scorpion toxin-like domain (Toxin_3) | Scorpion toxin-like domain | This family contains both neurotoxins and plant defensins. The mustard trypsin inhibitor, MTI-2, is plant defensin. It is a potent inhibitor of trypsin with no activity towards chymotrypsin. MTI-2 is toxic for Lepidopteran insects, but has low activ ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
---|---|---|---|---|
SINGLE CHAIN ANTIBODY FRAGMENT 9004G | - | - | - | |
SINGLE CHAIN ANTIBODY FRAGMENT 9004G | - | - | - | |
BETA-MAMMAL TOXIN CN2 |
|
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR036574 | Knottin, scorpion toxin-like superfamily | Homologous Superfamily | |
IPR018218 | Scorpion long chain toxin | Family | |
IPR002061 | Scorpion long chain toxin/defensin | Family | |
IPR003614 | Knottin, scorpion toxin-like | Domain | |
IPR044062 | LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain | Domain |
Membrane Protein Annotation: OPM OPM Database Homepage
Chains | External Link | Type | Class | Superfamily | Family |
---|---|---|---|---|---|
OPM | Monotopic/peripheral | Alpha + Beta monotopic/peripheral | Scorpion toxin-like knottin | Long-chain scorpion toxins |