Macromolecule Annotations for the Entities in PDB 1YYM

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
G86-492 d1yymg1 Alpha and beta proteins (a+b) gp120 core gp120 core gp120 core gp120 core Human immunodeficiency virus type 1 [TaxId: 11676]
H1-113 d1yymh1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH Human (Homo sapiens), cluster 1 [TaxId: 9606]
H114-214 d1yymh2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain- like) Immunoglobulin heavy chain gamma constant domain 1, CH1- gamma Human (Homo sapiens) [TaxId: 9606]
L1-107 d1yyml1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL- kappa Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
L108-212 d1yyml2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain- like) Immunoglobulin light chain kappa constant domain, CL- kappa Human (Homo sapiens) [TaxId: 9606]
P1086-1492 d1yymp1 Alpha and beta proteins (a+b) gp120 core gp120 core gp120 core gp120 core Human immunodeficiency virus type 1 [TaxId: 11676]
Q1001-1107 d1yymq1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL- kappa Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
Q1108-1212 d1yymq2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain- like) Immunoglobulin light chain kappa constant domain, CL- kappa Human (Homo sapiens) [TaxId: 9606]
R1001-1113 d1yymr1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH Human (Homo sapiens), cluster 1 [TaxId: 9606]
R1114-1214 d1yymr2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain- like) Immunoglobulin heavy chain gamma constant domain 1, CH1- gamma Human (Homo sapiens) [TaxId: 9606]
M2-27 d1yymm1 Designed proteins Scorpion toxin-based designs Scorpion toxin-based designs Mini-protein reproducing the core of the CD4 surface Mini-protein reproducing the core of the CD4 surface Synthetic
S1002-1027 d1yyms1 Designed proteins Scorpion toxin-based designs Scorpion toxin-based designs Mini-protein reproducing the core of the CD4 surface Mini-protein reproducing the core of the CD4 surface Synthetic

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source
H PF07686 V-set Immunoglobulin V-set domain Domain This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. PFAM PF07686
L PF07686 V-set Immunoglobulin V-set domain Domain This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. PFAM PF07686
H PF07654 C1-set Immunoglobulin C1-set domain Domain PFAM PF07654
G PF00516 GP120 Envelope glycoprotein GP120 Family
G PF00516 GP120 Envelope glycoprotein GP120 Family
L PF07654 C1-set Immunoglobulin C1-set domain Domain PFAM PF07654
G PF00516 GP120 Envelope glycoprotein GP120 Family

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
G,P Exterior membrane glycoprotein(GP120) (1YYM:G,P)
  • none
  • none
L,Q antibody 17b light chain (1YYM:L,Q)
  • none
  • none
  • none
H,R antibody 17b heavy chain (1YYM:H,R)
  • none
  • none
  • none
M,S F23, scorpion-toxin mimic of CD4 (1YYM:M,S)
  • none
  • none
  • none

Protein Modification Annotation

Type PDB Residue Nr. Description