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CRYSTAL STRUCTURE OF THE ADCC-POTENT, WEAKLY NEUTRALIZING HIV ENV CO-RECEPTOR BINDING SITE ANTIBODY N12-I2 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 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 e6w4mG1 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 e6w4mG2 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 L] C1-set_4 e6w4mL2 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) B [auth L] V-set e6w4mL1 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 [auth H] V-set_8 e6w4mH2 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 e6w4mH1 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 N] Toxin_2_like_1 e6w4mN1 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)
Chain Protein Name Description Organism Name Gene Allele Name(s) Domain Name(s) Receptor Type Receptor Description Provenance Source A [auth G] - LINKER - - - TR (LINKER) IMGT (202440-0) B [auth L] CLADE A/E 93TH057 HIV-1 GP120 CORE,L L-KAPPA - IGKV3-20*01, IGKJ1*01, IGKJ4*01, IGKJ2*01, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG (L-KAPPA_VH-CH1-HINGE-REGION) IMGT (202440-0) C [auth H] CLADE A/E 93TH057 HIV-1 GP120 CORE,L (VH-CH1-HINGE-REGION) - IGHV1-69*05, IGHJ6*01, IGHG1*03, IGHG1*08, IGHG1*06 V-DOMAIN VH, C-DOMAIN CH1 IG (L-KAPPA_VH-CH1-HINGE-REGION) IMGT (202440-0)
Chain Chain Class Chain Subclass Chain Type Antigen Name(s) Provenance Source B [auth L] Light Chain IGKV3 Kappa clade a/e 93th057 hiv-1 gp120 core | m48u1 cd4 mimetic peptide SAbDab (2024-10-11) C [auth H] Heavy Chain IGHV1 - clade a/e 93th057 hiv-1 gp120 core | m48u1 cd4 mimetic peptide SAbDab (2024-10-11)
Chains Polymer Molecular Function Biological Process Cellular Component A [auth G] clade A/E 93TH057 HIV-1 gp120 core - - B [auth L] ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN - - - C [auth H] ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN - - - D [auth N] M48U1 CD4 MIMETIC PEPTIDE - - -
Protein Modification Annotation Modified Residue(s) Chain Residue(s) Description C [auth H] TYS Parent Component: TYR RESID :  AA0172 PSI-MOD :  O4'-sulfo-L-tyrosine MOD:00181 D [auth N] DPR RESID :  AA0172 D [auth N] MPT RESID :  AA0172 D [auth N] NH2 RESID :  AA0172 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD :  O4'-sulfo-L-tyrosine MOD:00181 , 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 D [auth N] U2X Parent Component: TYR RESID :  AA0172 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100