5W4L
Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.
External Resource: Annotation
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| A [auth G] | SCOP2B Superfamily | gp120 core | 8096276 | 3001390 | SCOP2B (2022-06-29) |
| G [auth A] | SCOP2 Family | gp120 core | 8096275 | 4002534 | SCOP2 (2022-06-29) |
| G [auth A] | SCOP2 Superfamily | gp120 core | 8096276 | 3001390 | 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 G] | GP120_3rd | e5w4lG1 | 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 | e5w4lG2 | 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) |
| G [auth A] | GP120_3rd | e5w4lA2 | 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) |
| G [auth A] | GP120_1st | e5w4lA1 | 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 | e5w4lN1 | 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) |
| H [auth M] | Toxin_2_like_1 | e5w4lM1 | 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 | e5w4lH2 | 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 | e5w4lH1 | 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) |
| I [auth F] | V-set_8 | e5w4lF1 | 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) |
| I [auth F] | C1-set_1 | e5w4lF2 | 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 | e5w4lL1 | 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 | e5w4lL2 | 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) |
| J [auth I] | C1-set | e5w4lI2 | 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) |
| J [auth I] | V-set_3 | e5w4lI1 | 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) |
| E [auth D] | V-set_8 | e5w4lD2 | 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 D] | C1-set_1 | e5w4lD1 | 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) |
| K [auth B] | V-set_8 | e5w4lB1 | 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) |
| K [auth B] | C1-set_1 | e5w4lB2 | 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 E] | C1-set_4 | e5w4lE1 | 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 E] | V-set | e5w4lE2 | 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) |
| L [auth C] | C1-set_4 | e5w4lC2 | 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) |
| L [auth C] | V-set | e5w4lC1 | 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) |
|---|---|---|---|---|---|---|
| C [auth H] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| I [auth F] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| D [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| J [auth I] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| E [auth D] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| K [auth B] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| F [auth E] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| L [auth C] | 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 |
|---|---|---|---|---|---|---|---|---|
| C [auth H], I [auth F] | Fab N5-i5 | VH-CH1 | Homo sapiens (human) | IGHV3-23*04, IGHJ4*01, IGHJ4*02, IGHJ4*03, IGHG1*03 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_LAMBDA | IMGT (202415-0) |
| D [auth L], J [auth I] | Fab N5-i5 | L-LAMBDA | Homo sapiens (human) | IGLV2-23*02, IGLJ2*01, IGLJ3*02, IGLJ1*01, IGLJ3*01, IGLC2*01, IGLC2*02, IGLC3*04 | V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA | IG | FAB-GAMMA-1_LAMBDA | IMGT (202415-0) |
| E [auth D], K [auth B] | Fab N12-i3 | VH-CH1 | Homo sapiens (human) | IGHV1-69*01, IGHV1-69*02, IGHV1-69*08, IGHV1-69*11, IGHV1-69*12, IGHV1-69*13, IGHV1-69D*01, IGHJ3*01, IGHG1*03 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202415-0) |
| F [auth E], L [auth C] | Fab N12-i3 | L-KAPPA | Homo sapiens (human) | IGKV3-20*01, IGKJ4*01, IGKJ4*02, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202415-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
| Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
|---|---|---|---|---|---|
| C [auth H], I [auth F] | Heavy Chain | IGHV3 | - | clade a/e 93th057 hiv-1 gp120 core | SAbDab (2024-04-19) |
| D [auth L], J [auth I] | Light Chain | IGLV2 | Lambda | clade a/e 93th057 hiv-1 gp120 core | SAbDab (2024-04-19) |
| E [auth D], K [auth B] | Heavy Chain | IGHV1 | - | clade a/e 93th057 hiv-1 gp120 core | SAbDab (2024-04-19) |
| F [auth E], L [auth C] | Light Chain | IGKV3 | Kappa | clade a/e 93th057 hiv-1 gp120 core | SAbDab (2024-04-19) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| A [auth G], G [auth A] | PF00516 | Envelope glycoprotein GP120 (GP120) | Envelope glycoprotein GP120 | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
| Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
|---|---|---|---|---|
| A [auth G], G [auth A] | clade A/E 93TH057 HIV-1 gp120 core | - | - | |
| B [auth N], H [auth M] | CD4 mimetic peptide M48U1 | - | - | - |
| C [auth H], I [auth F] | Antibody N5-i5 Fab heavy chain | - | - | - |
| D [auth L], J [auth I] | Antibody N5-i5 light chain | - | - | - |
| E [auth D], K [auth B] | Antibody N12-i3 Fab heavy chain | - | - | - |
| F [auth E], L [auth C] | Antibody N12-i3 light chain | - | - | - |
InterPro: Protein Family Classification InterPro Database Homepage
| Chains | Accession | Name | Type |
|---|---|---|---|
| A [auth G], G [auth A] | IPR000777 | Human immunodeficiency virus 1, envelope glycoprotein Gp120 | Domain |
| A [auth G], G [auth A] | IPR036377 | Gp120 core superfamily | Homologous Superfamily |
Protein Modification Annotation
| Modified Residue(s) | ||
|---|---|---|
| Chain | Residue(s) | Description |
| B [auth N], H [auth M] | DPR | |
| B [auth N], H [auth M] | MPT | |
| B [auth N], H [auth M] | NH2 | : AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 : 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], H [auth M] | U2X | Parent Component: TYR : AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 |
