5VN3
Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B [auth A] | SCOP2B Superfamily | Virus ectodomain | 8085612 | 3001628 | SCOP2B (2021-05-27) |
G [auth B] | SCOP2B Superfamily | Virus ectodomain | 8085612 | 3001628 | SCOP2B (2021-05-27) |
L [auth D] | SCOP2B Superfamily | Virus ectodomain | 8085612 | 3001628 | SCOP2B (2021-05-27) |
C [auth G] | SCOP2B Superfamily | gp120 core | 8097270 | 3001390 | SCOP2B (2021-05-27) |
H [auth I] | SCOP2B Superfamily | gp120 core | 8097270 | 3001390 | SCOP2B (2021-05-27) |
M [auth J] | SCOP2B Superfamily | gp120 core | 8097270 | 3001390 | SCOP2B (2021-05-27) |
D [auth C] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8054493 | 3000071 | SCOP2B (2021-05-27) |
D [auth C] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8054739 | 3000071 | SCOP2B (2021-05-27) |
I [auth E] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8054739 | 3000071 | SCOP2B (2021-05-27) |
I [auth E] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8054493 | 3000071 | SCOP2B (2021-05-27) |
N [auth F] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8054493 | 3000071 | SCOP2B (2021-05-27) |
N [auth F] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8054739 | 3000071 | SCOP2B (2021-05-27) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth L] | PF07686 | e5vn3L1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
F [auth N] | PF07686 | e5vn3N1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
K [auth O] | PF07686 | e5vn3O1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
B [auth A] | PF00517 | e5vn3A1 | A: a+b duplicates or obligate multimers | X: MPER trimer (From Topology) | H: MPER trimer (From Topology) | T: MPER trimer | F: PF00517 | ECOD (1.6) |
G [auth B] | PF00517 | e5vn3B1 | A: a+b duplicates or obligate multimers | X: MPER trimer (From Topology) | H: MPER trimer (From Topology) | T: MPER trimer | F: PF00517 | ECOD (1.6) |
L [auth D] | PF00517 | e5vn3D1 | A: a+b duplicates or obligate multimers | X: MPER trimer (From Topology) | H: MPER trimer (From Topology) | T: MPER trimer | F: PF00517 | ECOD (1.6) |
C [auth G] | F_UNCLASSIFIED | e5vn3G1 | A: beta barrels | X: V1/V2 domain in HIV gp120 (From Topology) | H: V1/V2 domain in HIV gp120 (From Topology) | T: V1/V2 domain in HIV gp120 | F: F_UNCLASSIFIED | ECOD (1.6) |
C [auth G] | PF00516 | e5vn3G3 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: PF00516 | ECOD (1.6) |
C [auth G] | PF00516 | e5vn3G2 | A: a+b two layers | X: gp120 inner domain (From Topology) | H: gp120 inner domain (From Topology) | T: gp120 inner domain | F: PF00516 | ECOD (1.6) |
H [auth I] | F_UNCLASSIFIED | e5vn3I1 | A: beta barrels | X: V1/V2 domain in HIV gp120 (From Topology) | H: V1/V2 domain in HIV gp120 (From Topology) | T: V1/V2 domain in HIV gp120 | F: F_UNCLASSIFIED | ECOD (1.6) |
H [auth I] | PF00516 | e5vn3I2 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: PF00516 | ECOD (1.6) |
H [auth I] | PF00516 | e5vn3I3 | A: a+b two layers | X: gp120 inner domain (From Topology) | H: gp120 inner domain (From Topology) | T: gp120 inner domain | F: PF00516 | ECOD (1.6) |
M [auth J] | F_UNCLASSIFIED | e5vn3J3 | A: beta barrels | X: V1/V2 domain in HIV gp120 (From Topology) | H: V1/V2 domain in HIV gp120 (From Topology) | T: V1/V2 domain in HIV gp120 | F: F_UNCLASSIFIED | ECOD (1.6) |
M [auth J] | PF00516 | e5vn3J2 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: PF00516 | ECOD (1.6) |
M [auth J] | PF00516 | e5vn3J1 | A: a+b two layers | X: gp120 inner domain (From Topology) | H: gp120 inner domain (From Topology) | T: gp120 inner domain | F: PF00516 | ECOD (1.6) |
D [auth C] | PF00047 | e5vn3C2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF00047 | ECOD (1.6) |
D [auth C] | PF05790 | e5vn3C1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF05790 | ECOD (1.6) |
I [auth E] | PF00047 | e5vn3E1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF00047 | ECOD (1.6) |
I [auth E] | PF05790 | e5vn3E2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF05790 | ECOD (1.6) |
N [auth F] | PF00047 | e5vn3F2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF00047 | ECOD (1.6) |
N [auth F] | PF05790 | e5vn3F1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF05790 | ECOD (1.6) |
O [auth M] | PF07686 | e5vn3M1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
E [auth H] | PF07686 | e5vn3H1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
J [auth K] | PF07686 | e5vn3K1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
F [auth N] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
K [auth O] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
C [auth G] | 2.170.40.20 | Mainly Beta | Beta Complex | HIV Envelope Protein Gp120 | Chain G | CATH (4.3.0) |
H [auth I] | 2.170.40.20 | Mainly Beta | Beta Complex | HIV Envelope Protein Gp120 | Chain G | CATH (4.3.0) |
M [auth J] | 2.170.40.20 | Mainly Beta | Beta Complex | HIV Envelope Protein Gp120 | Chain G | CATH (4.3.0) |
D [auth C] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
I [auth E] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
N [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 |
---|---|---|---|---|---|---|---|---|
A [auth L], F [auth N], K [auth O] | Fab 17b | L-KAPPA | Homo sapiens (human) | IGKV3-15*01, IGKV3D-15*01, IGKJ5*01, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202428-2) |
E [auth H], J [auth K], O [auth M] | Fab 17b | VH-CH1 | Homo sapiens (human) | IGHV1-69*02, IGHV1-69*04, IGHV1-69*08, IGHV1-69*09, IGHJ5*01, IGHJ5*02, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05, IGHG1*12, IGHG1*14, IGHG1*13, IGHG1*09, IGHG1*10, IGHG1*07, IGHG1*11 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202428-2) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
A [auth L], F [auth N], K [auth O] | Light Chain | IGKV3 | Kappa | envelope glycoprotein gp160 | SAbDab (2024-07-12) |
E [auth H], J [auth K], O [auth M] | Heavy Chain | IGHV1 | - | envelope glycoprotein gp160 | SAbDab (2024-07-12) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
B [auth A], G [auth B], L [auth D] | PF00517 | Retroviral envelope protein (GP41) | Retroviral envelope protein | - | Family |
C [auth G], H [auth I], M [auth J] | PF00516 | Envelope glycoprotein GP120 (GP120) | Envelope glycoprotein GP120 | - | Family |
D [auth C], I [auth E], N [auth F] | PF05790 | Immunoglobulin C2-set domain (C2-set) | Immunoglobulin C2-set domain | - | Domain |
D [auth C], I [auth E], N [auth F] | PF00047 | Immunoglobulin domain (ig) | Immunoglobulin domain | Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prot ... | Domain |