1RZK	Viral Protein Immune System	date	Dec 24, 2003
title	Hiv-1 Yu2 Gp120 Envelope Glycoprotein Complexed With Cd4 And Neutralizing Antibody 17b
authors	C.C.Huang, M.Venturi, S.Majeed, M.J.Moore, S.Phogat, M.Y.Zhang, D.S.Dimitrov, W.A.Hendrickson, J.Robinson, J.Sodroski, R.Wyatt, M.Farzan, P.D.Kwong
compound		source
Molecule: Envelope Glycoprotein Gp120 Chain: G Fragment: Core Engineered: Yes Mutation: Yes Other_details: Part Of Envelope Polyprotein Gp160		Organism_scientific: Human Immunodeficiency Virus 1 Organism_taxid: 11676 Strain: Clade B Variant: Laboratory-Adapted Isolate Hxbc2 Expression_system: Drosophila Melanogaster Expression_system_common: Fruit Fly Expression_system_taxid: 7227 Other_details: Secreted From Drosophila Schneider 2 Lines U Control Of An Inducible Metallothionein Promoter;
Molecule: T-Cell Surface Glycoprotein Cd4 Chain: C Fragment: D1d2, N-Terminal Two Domain Fragment Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_cell: Ovary Cells (Cho)
Molecule: Antibody 17b, Light Chain Chain: L 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 Expression_system_cell: Immortalized B-Cell Clone Fused Wit Murine B-Cell Fusion Partner;
Molecule: Antibody 17b, Heavy Chain Chain: H 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 Expression_system_cell: Immortalized B-Cell Clone Fused Wit Murine B-Cell Fusion Partner
symmetry	Space Group: C 1 2 1	R_factor 0.205 R_Free 0.297
crystal cell	length a length b length c angle alpha angle beta angle gamma 174.980 81.710 74.480 90.00 90.37 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	NAG	enzyme
related structures	by homologous chain: 1B4J, 1CDI, 1FH5, 1G9N, 1YYL
Gene Ontology	Chain Function Process Component C G
Primary reference	Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120., Huang CC, Venturi M, Majeed S, Moore MJ, Phogat S, Zhang MY, Dimitrov DS, Hendrickson WA, Robinson J, Sodroski J, Wyatt R, Choe H, Farzan M, Kwong PD, Proc Natl Acad Sci U S A 2004 Mar 2;101(9):2706-11. Epub 2004 Feb 23. PMID:14981267

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk] Biological Unit Coordinates (1rzk.pdb1.gz) 156 Kb LPC: Ligand-Protein Contacts for 1RZK CSU: Contacts of Structural Units for 1RZK Likely Quarternary Molecular Structure file(s) for 1RZK Structure Factors (239 Kb) Retrieve 1RZK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RZK from S2C, [Save to disk] Re-refined 1rzk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RZK 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 1RZK

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 1RZK, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rzkc1, region C:1-97 [Jmol] [rasmolscript] [script source]     - Domain d1rzkc2, region C:98-181 [Jmol] [rasmolscript] [script source]     - Domain d1rzkg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1rzkh1, region H:1-113 [Jmol] [rasmolscript] [script source]     - Domain d1rzkh2, region H:114-214 [Jmol] [rasmolscript] [script source]     - Domain d1rzkl1, region L:1-109 [Jmol] [rasmolscript] [script source]     - Domain d1rzkl2, region L:110-212 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rzk_L] [1rzk_H] [1rzk] [1rzk_C] [1rzk_G] SWISS-PROT database: [P01730] Domain organization of [CD4_HUMAN] by SWISSPFAM Domains found in 1RZK: [IG_like] [IGv ] by SMART

Other resources with information on 1RZK

Community annotation for 1RZK at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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