1YYM Viral Protein Immune System date Feb 25, 2005
title Crystal Structure Of F23, A Scorpion-Toxin Mimic Of Cd4, In With Hiv-1 Yu2 Gp120 Envelope Glycoprotein And Anti-Hiv-1 A 17b
authors C.C.Huang, F.Stricher, L.Martin, J.M.Decker, S.Majeed, P.Barthe, W.A.Hendrickson, J.Robinson, C.Roumestand, J.Sodroski, R.Wyatt, C.Vita, P.D.Kwong
compound source
Molecule: Exterior Membrane Glycoprotein(Gp120),Exterior Me Glycoprotein(Gp120),Exterior Membrane Glycoprotein(Gp120);
Chain: G, P
Fragment: Unp Residues 82-126,Unp Residues 191-293,Unp Resi 479;
Synonym: Hiv-1 Yu2 Gp120, Envelope Glycoprotein Gp160,Hiv-1 Gp120, Envelope Glycoprotein Gp160,Hiv-1 Yu2 Gp120, Envelop Glycoprotein Gp160;
Engineered: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227

Molecule: Antibody 17b Light Chain
Chain: L, Q
Fragment: Antigen-Binding Fragment, Fab
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Mus Musculus
Expression_system_common: Mouse
Expression_system_taxid: 10090
Other_details: Epstein-Barr Virus Immortalized B-Cellclone With A Murine B-Cell Fusion Partner;

Molecule: Antibody 17b Heavy Chain
Chain: H, R
Fragment: Antigen-Binding Fragment, Fab
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Mus Musculus
Expression_system_common: Mouse
Expression_system_taxid: 10090
Other_details: Epstein-Barr Virus Immortalized B-Cellclone With A Murine B-Cell Fusion Partner;

Molecule: F23, Scorpion-Toxin Mimic Of Cd4
Chain: M, S
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Miniprotein (Solid Phase Method Us Protected Amino Acids)
symmetry Space Group: P 1 21 1
R_factor 0.209 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.620 157.041 108.929 90.00 93.45 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand EDO, IPA, MPT, NAG, VLM enzyme
note 1YYM is a representative structure
related structures by homologous chain: 1KCU, 1RZJ, 1TJI, 1TZG
Gene
Ontology
ChainFunctionProcessComponent
P, G


Primary referenceScorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth., Huang CC, Stricher F, Martin L, Decker JM, Majeed S, Barthe P, Hendrickson WA, Robinson J, Roumestand C, Sodroski J, Wyatt R, Shaw GM, Vita C, Kwong PD, Structure. 2005 May;13(5):755-68. PMID:15893666
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (263 Kb) [Save to disk]
  • Biological Unit Coordinates (1yym.pdb1.gz) 131 Kb
  • Biological Unit Coordinates (1yym.pdb2.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 1YYM
  • CSU: Contacts of Structural Units for 1YYM
  • Likely Quarternary Molecular Structure file(s) for 1YYM
  • Structure Factors (1255 Kb)
  • Retrieve 1YYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YYM from S2C, [Save to disk]
  • Re-refined 1yym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YYM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1YYM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YYM, from MSDmotif at EBI
  • Fold representative 1yym from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yym_Q] [1yym_R] [1yym_P] [1yym_S] [1yym_L] [1yym_H] [1yym_M] [1yym_G] [1yym]
  • SWISS-PROT database: [P35961]
  • Domain organization of [ENV_HV1Y2] by SWISSPFAM
  • Domains found in 1YYM: [IG_like] [IGv ] by SMART
  • Other resources with information on 1YYM
  • Community annotation for 1YYM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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