2NY1 Viral Protein Immune System date Nov 20, 2006
title Hiv-1 Gp120 Envelope Glycoprotein (I109c, T257s, S334a, S375 Complexed With Cd4 And Antibody 17b
authors T.Zhou, L.Xu, B.Dey, A.J.Hessell, D.Van Ryk, S.H.Xiang, X.Yang, M.Y M.B.Zwick, J.Arthos, D.R.Burton, D.S.Dimitrov, J.Sodroski, R.Wya G.J.Nabel, P.D.Kwong
compound source
Molecule: Envelope Glycoprotein Gp120
Chain: A
Fragment: Core
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Strain: Hxbc2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Embryonic Cell Line 293
Expression_system_organ: Kidney
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Cmvr

Molecule: T-Cell Surface Glycoprotein Cd4
Chain: B
Fragment: D1d2, N-Terminal Two Domain Fragment
Synonym: T-Cell Surface Antigen T4leu-3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Epstein-Barr Virus Immortalize Clone Fused With A Murine B-Cell Fusion Partner;

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Epstein-Barr Virus Immortalize Clone Fused With A Murine B-Cell Fusion Partner
symmetry Space Group: P 2 2 21
R_factor 0.209 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.113 88.156 197.672 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.99 Å
ligand FRU, GLC, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural definition of a conserved neutralization epitope on HIV-1 gp120., Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, Kwong PD, Nature. 2007 Feb 15;445(7129):732-7. PMID:17301785
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (315 Kb) [Save to disk]
  • Biological Unit Coordinates (2ny1.pdb1.gz) 306 Kb
  • LPC: Ligand-Protein Contacts for 2NY1
  • CSU: Contacts of Structural Units for 2NY1
  • Likely Quarternary Molecular Structure file(s) for 2NY1
  • Structure Factors (1826 Kb)
  • Retrieve 2NY1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NY1 from S2C, [Save to disk]
  • Re-refined 2ny1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NY1 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 2NY1
  • 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 2NY1, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ny1_D] [2ny1_B] [2ny1_C] [2ny1_A] [2ny1]
  • SWISS-PROT database: [P01730] [Q6N030] [Q6P5S8] [Q993A8]
  • Domain organization of [CD4_HUMAN] [Q6N030_HUMAN] [Q6P5S8_HUMAN] [Q993A8_9HIV1] by SWISSPFAM
  • Domains found in 2NY1: [IG_like] [IGv ] by SMART
  • Other resources with information on 2NY1
  • Community annotation for 2NY1 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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