3Q1S Immune System Cytokine date Dec 17, 2010
title Hiv-1 Neutralizing Antibody Z13e1 In Complex With Epitope Di Protein
authors R.L.Stanfield, J.P.Julien, R.Pejchal, J.S.Gach, M.B.Zwick, I.A.W
compound source
Molecule: Z13e1 Fab Light Chain
Chain: L
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Z13e1 Fab Heavy Chain
Chain: H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Interleukin-22
Chain: I
Fragment: Unp Residues 29-179
Synonym: Il-22, Cytokine Zcyto18, Il-10-Related T-Cell-Deri Inducible Factor, Il-Tif;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il22, Iltif, Zcyto18, Unq3099pro10096
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
56.623 99.216 105.533 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand GOL, IPA enzyme

Primary referenceStructure-Based Design of a Protein Immunogen that Displays an HIV-1 gp41 Neutralizing Epitope., Stanfield RL, Julien JP, Pejchal R, Gach JS, Zwick MB, Wilson IA, J Mol Biol. 2011 Dec 2;414(3):460-76. Epub 2011 Oct 15. PMID:22033480
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk]
  • Biological Unit Coordinates (3q1s.pdb1.gz) 179 Kb
  • LPC: Ligand-Protein Contacts for 3Q1S
  • CSU: Contacts of Structural Units for 3Q1S
  • Structure Factors (211 Kb)
  • Retrieve 3Q1S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3Q1S from S2C, [Save to disk]
  • Re-refined 3q1s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3Q1S 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 3Q1S
  • 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 3Q1S, from MSDmotif at EBI
  • Fold representative 3q1s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3q1s_I] [3q1s_H] [3q1s_L] [3q1s]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3Q1S: [IG_like] [IGv] [IL10 ] by SMART
  • Other resources with information on 3Q1S
  • Community annotation for 3Q1S at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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