3IDY	Immune System	date	Jul 22, 2009
title	Crystal Structure Of Hiv-Gp120 Core In Complex With Cd4-Bind Antibody B13, Space Group C2221
authors	L.Chen, Y.D.Kwon, T.Zhou, X.Wu, S.O'Dell, L.Cavacini, A.J.Hessell, M.Pancera, M.Tang, L.Xu, Z.Y.Yang, M.Y.Zhang, J.Arthos, D.R.Burto D.S.Dimitrov, G.J.Nabel, M.Posner, J.Sodroski, R.Wyatt, J.R.Masc P.D.Kwong
compound		source
Molecule: Hiv-1 Hxbc2 Gp120 Core Chain: G, A Engineered: Yes Mutation: Yes		Organism_scientific: Human Immunodeficiency Virus 1 Organism_taxid: 11676 Strain: Hxbc2 Gene: Env Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcdna3.1(-)
Molecule: Fab B13 Heavy Chain Chain: H, B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcdna3.1(-)
Molecule: Fab B13 Light Chain Chain: L, C Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcdna3.1(-)
symmetry	Space Group: C 2 2 21	R_factor 0.196 R_Free 0.237
crystal cell	length a length b length c angle alpha angle beta angle gamma 106.168 204.316 216.886 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.20 Å
ligand	NAG, SO4	enzyme
Gene Ontology	Chain Function Process Component A, G
Primary reference	Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120., Chen L, Do Kwon Y, Zhou T, Wu X, O'Dell S, Cavacini L, Hessell AJ, Pancera M, Tang M, Xu L, Yang ZY, Zhang MY, Arthos J, Burton DR, Dimitrov DS, Nabel GJ, Posner MR, Sodroski J, Wyatt R, Mascola JR, Kwong PD, Science. 2009 Nov 20;326(5956):1123-7. PMID:19965434

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (515 Kb) [Save to disk] Biological Unit Coordinates (3idy.pdb1.gz) 506 Kb Biological Unit Coordinates (3idy.pdb2.gz) 506 Kb LPC: Ligand-Protein Contacts for 3IDY CSU: Contacts of Structural Units for 3IDY Structure Factors (513 Kb) Retrieve 3IDY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3IDY from S2C, [Save to disk] Re-refined 3idy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3IDY 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 3IDY

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 3IDY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3idy_G] [3idy_B] [3idy_L] [3idy_H] [3idy] [3idy_C] [3idy_A] SWISS-PROT database: [P04578] Belongs to the human immunodeficiency virus type 1 (hiv-1) fusion peptide (hiv-fp) family according to TCDB. Domain organization of [ENV_HV1H2] by SWISSPFAM Domains found in 3IDY: [IG_like] [IGv ] by SMART

Other resources with information on 3IDY

Community annotation for 3IDY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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