2I5Y	Viral Protein Immune System	date	Aug 26, 2006
title	Crystal Structure Of Cd4m47, A Scorpion-Toxin Mimic Of Cd4, With Hiv-1 Yu2 Gp120 Envelope Glycoprotein And Anti-Hiv-1 A 17b
authors	C.C.Huang, P.D.Kwong
compound		source
Molecule: Exterior Membrane Glycoprotein(Gp120) Chain: G, P Fragment: Core Synonym: Hiv-1 Yu2 Gp120 Engineered: Yes		Organism_scientific: Human Immunodeficiency Virus Organism_taxid: 12721 Strain: Yu2 Gene: Env 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: Human Herpesvirus 4 Expression_system_common: Epstein-Barr Virus Expression_system_taxid: 10376
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: Human Herpesvirus 4 Expression_system_common: Epstein-Barr Virus Expression_system_taxid: 10376
Molecule: Cd4m47, Scorpion-Toxin Mimic Of Cd4 Chain: M, S Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Organism_taxid: 32630 Other_details: This Protein Is A Mimic Of The Protein That Naturally In Leiurus Quinquestriatus Hebraeus (Israeli Scor
symmetry	Space Group: P 1 21 1	R_factor 0.214 R_Free 0.273
crystal cell	length a length b length c angle alpha angle beta angle gamma 51.437 158.160 109.933 90.00 93.67 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	BIF, DPR, MPT, NAG, VLM	enzyme
Gene Ontology	Chain Function Process Component P, G
Primary reference	Combinatorial optimization of a CD4-mimetic miniprotein and cocrystal structures with HIV-1 gp120 envelope glycoprotein., Stricher F, Huang CC, Descours A, Duquesnoy S, Combes O, Decker JM, Kwon YD, Lusso P, Shaw GM, Vita C, Kwong PD, Martin L, J Mol Biol. 2008 Oct 3;382(2):510-24. Epub 2008 Jul 1. PMID:18619974

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (257 Kb) [Save to disk] Biological Unit Coordinates (2i5y.pdb1.gz) 129 Kb Biological Unit Coordinates (2i5y.pdb2.gz) 126 Kb LPC: Ligand-Protein Contacts for 2I5Y CSU: Contacts of Structural Units for 2I5Y Likely Quarternary Molecular Structure file(s) for 2I5Y Structure Factors (1107 Kb) Retrieve 2I5Y in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2I5Y from S2C, [Save to disk] Re-refined 2i5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2I5Y 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 2I5Y

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 3D motif for 2I5Y, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2i5y_R] [2i5y_H] [2i5y_G] [2i5y_L] [2i5y_M] [2i5y_S] [2i5y_Q] [2i5y] [2i5y_P] SWISS-PROT database: [P35961] [P01857] Domain organization of [ENV_HV1Y2] [IGHG1_HUMAN] by SWISSPFAM Domains found in 2I5Y: [IG_like] [IGv ] by SMART

Other resources with information on 2I5Y

Community annotation for 2I5Y at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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