Crystal structure of the ADCC-potent antibody N60-i3 Fab in complex with HIV-1 Clade A/E gp120 W69A/S115W mutant and M48U1.
External Resource: Annotation
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
A [auth G] | SCOP2B Superfamily | gp120 core | 8096276 | 3001390 | SCOP2B (2022-06-29) |
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
A [auth G] | GP120_3rd | e5kjrG2 | 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: GP120_3rd | ECOD (1.6) |
A [auth G] | GP120_1st | e5kjrG1 | A: a+b two layers | X: gp120 inner domain (From Topology) | H: gp120 inner domain (From Topology) | T: gp120 inner domain | F: GP120_1st | ECOD (1.6) |
B [auth N] | Toxin_2_like_1 | e5kjrN1 | A: few secondary structure elements | X: omega toxin-like | H: omega toxin-related | T: Scorpion toxin-like | F: Toxin_2_like_1 | ECOD (1.6) |
C [auth H] | V-set_8 | e5kjrH2 | 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) |
C [auth H] | C1-set_1 | e5kjrH1 | 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) |
D [auth L] | C1-set | e5kjrL1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set | ECOD (1.6) |
D [auth L] | V-set_3 | e5kjrL2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_3 | ECOD (1.6) |
Chain | Protein Name | Description | Organism Name | Gene Allele Name(s) | Domain Name(s) | Receptor Type | Receptor Description | Provenance Source |
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C [auth H] | N60-I3 Fab | VH-CH1 | Homo sapiens (human) | IGHV4-31*02, IGHV4-31*03, IGHJ5*01, IGHG1*03 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_LAMBDA | IMGT (202436-0) |
D [auth L] | N60-I3 Fab | L-LAMBDA | Homo sapiens (human) | IGLV2-14*01, IGLJ3*02, IGLC2*01, IGLC2*02, IGLC3*04 | V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA | IG | FAB-GAMMA-1_LAMBDA | IMGT (202436-0) |
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
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C [auth H] | Heavy Chain | IGHV4 | - | clade a/e 93th057 hiv-1 gp120 core | SAbDab (2024-09-13) |
D [auth L] | Light Chain | IGLV2 | Lambda | clade a/e 93th057 hiv-1 gp120 core | SAbDab (2024-09-13) |
Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
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A [auth G] | clade A/E 93TH057 HIV-1 gp120 core | - | - | |
B [auth N] | M48U1 CD4 MIMETIC PEPTIDE | - | - | - |
C [auth H] | N60-I3 FAB HEAVY CHAIN | - | - | - |
D [auth L] | N60-I3 FAB LIGHT CHAIN | - | - | - |
Protein Modification Annotation
Modified Residue(s) |
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Chain | Residue(s) | Description |
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B [auth N] | DPR | |
B [auth N] | MPT | |
B [auth N] | NH2 | RESID:  AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100
PSI-MOD :  L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109 |
B [auth N] | U2X | Parent Component: TYR
RESID:  AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100
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