5K59
Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody
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
- Thera-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: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth D] | SCOP2B Superfamily | Leukocidin-like | 8099272 | 3000256 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Leukocidin-like | 8099272 | 3000256 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Leukocidin-like | 8074050 | 3000256 | SCOP2B (2022-06-29) |
D [auth A] | SCOP2 Family | Leukocidin (pore-forming toxin) | 8074049 | 4003101 | SCOP2 (2022-06-29) |
D [auth A] | SCOP2 Superfamily | Leukocidin-like | 8074050 | 3000256 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth D] | Leukocidin | e5k59D1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Leukocidin-like (From Topology) | T: Leukocidin-like | F: Leukocidin | ECOD (1.6) |
C | Leukocidin | e5k59C1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Leukocidin-like (From Topology) | T: Leukocidin-like | F: Leukocidin | ECOD (1.6) |
B | Leukocidin | e5k59B1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Leukocidin-like (From Topology) | T: Leukocidin-like | F: Leukocidin | ECOD (1.6) |
D [auth A] | Leukocidin | e5k59A1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Leukocidin-like (From Topology) | T: Leukocidin-like | F: Leukocidin | ECOD (1.6) |
E [auth H] | V-set_8 | e5k59H2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_8 | ECOD (1.6) |
E [auth H] | C1-set_1 | e5k59H1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set_1 | ECOD (1.6) |
G [auth E] | V-set_8 | e5k59E1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_8 | ECOD (1.6) |
G [auth E] | C1-set_1 | e5k59E2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set_1 | ECOD (1.6) |
F [auth L] | C1-set_4 | e5k59L1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set_4 | ECOD (1.6) |
F [auth L] | V-set | e5k59L2 | 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) |
H [auth F] | C1-set_4 | e5k59F1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set_4 | ECOD (1.6) |
H [auth F] | V-set | e5k59F2 | 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) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A [auth D] | 2.70.240.10 | Mainly Beta | Distorted Sandwich | Leukocidin-like | Leukocidin/porin MspA | CATH (4.3.0) |
C | 2.70.240.10 | Mainly Beta | Distorted Sandwich | Leukocidin-like | Leukocidin/porin MspA | CATH (4.3.0) |
B | 2.70.240.10 | Mainly Beta | Distorted Sandwich | Leukocidin-like | Leukocidin/porin MspA | CATH (4.3.0) |
D [auth A] | 2.70.240.10 | Mainly Beta | Distorted Sandwich | Leukocidin-like | Leukocidin/porin MspA | CATH (4.3.0) |
E [auth H] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
G [auth E] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
F [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
H [auth F] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | 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 |
---|---|---|---|---|---|---|---|---|
E [auth H], G [auth E] | Antibody Fab Fragment | VH-CH1 | Homo sapiens (human) | IGHV4-39*01, IGHV4-39*06, IGHV4-39*07, IGHJ6*04, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202444-0) |
F [auth L], H [auth F] | Antibody Fab Fragment | L-KAPPA | Homo sapiens (human) | IGKV1-39*01, IGKV1D-39*01, IGKJ4*01, IGKJ4*02, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202444-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
E [auth H], G [auth E] | Heavy Chain | IGHV4 | - | uncharacterized leukocidin-like protein 1 | SAbDab (2024-11-08) |
F [auth L], H [auth F] | Light Chain | IGKV1 | Kappa | uncharacterized leukocidin-like protein 1 | SAbDab (2024-11-08) |
Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage
Chain | Name | Target | Provenance Source |
---|---|---|---|
E [auth H], G [auth E] | Berlimatoxumab | Staphylococcus aureus Toxin A | Therapeutic SAbDab (2024-11-08) |
F [auth L], H [auth F] | Berlimatoxumab | Staphylococcus aureus Toxin A | Therapeutic SAbDab (2024-11-08) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth D], C | PF07968 | Leukocidin/Hemolysin toxin family (Leukocidin) | Leukocidin/Hemolysin toxin family | - | Domain |
B, D [auth A] | PF07968 | Leukocidin/Hemolysin toxin family (Leukocidin) | Leukocidin/Hemolysin toxin family | - | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
---|---|---|---|---|
A [auth D], C | Uncharacterized leukocidin-like protein 2 | - | ||
B, D [auth A] | Uncharacterized leukocidin-like protein 1 | - | ||
E [auth H], G [auth E] | Fab heavy chain | - | - | - |
F [auth L], H [auth F] | Fab light chain | - | - | - |
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
A [auth D], C | IPR016183 | Leukocidin/Hemolysin toxin | Domain |
A [auth D], C | IPR036435 | Leukocidin/porin MspA superfamily | Homologous Superfamily |
A [auth D], C | IPR003963 | Bi-component toxin, staphylococci | Family |
B, D [auth A] | IPR016183 | Leukocidin/Hemolysin toxin | Domain |
B, D [auth A] | IPR036435 | Leukocidin/porin MspA superfamily | Homologous Superfamily |
B, D [auth A] | IPR003963 | Bi-component toxin, staphylococci | Family |
Membrane Protein Annotation: OPM OPM Database Homepage
Chains | External Link | Type | Class | Superfamily | Family |
---|---|---|---|---|---|
OPM | Transmembrane | Beta-barrel transmembrane | Pore-forming beta-sheet toxins | Aerolysin (n=14,S=14 or n=16,S=16) |