6D2P Immune System date Apr 13, 2018
title Crystal Structure Of Ioma-Class Clk31 Fab From An Hiv-1 Naiv Complex With A Germline-Targeting Gp120 Engineered Outer Do Gt8 At 2.6 A
authors A.Sarkar, I.A.Wilson
compound source
Molecule: Germline-Targeting Hiv-1 Gp120 Engineered Outer D Gt8;
Chain: C
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: Hek 293s
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phlsec

Molecule: Iomaclass Naive Clk31 Fab Heavy Chain
Chain: H
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: Hek 293 Freestyle
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfusess-Chig-Hg1

Molecule: Iomaclass Naive Clk31 Fab Light Chain
Chain: L
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: Hek 293 Freestyle
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfusess-Chig-Hg1
symmetry Space Group: P 21 21 2
R_factor 0.213 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.300 66.636 76.518 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


Primary referenceThe human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen., Havenar-Daughton C, Sarkar A, Kulp DW, Toy L, Hu X, Deresa I, Kalyuzhniy O, Kaushik K, Upadhyay AA, Menis S, Landais E, Cao L, Diedrich JK, Kumar S, Schiffner T, Reiss SM, Seumois G, Yates JR, Paulson JC, Bosinger SE, Wilson IA, Schief WR, Crotty S, Sci Transl Med. 2018 Jul 4;10(448). pii: 10/448/eaat0381. doi:, 10.1126/scitranslmed.aat0381. PMID:29973404
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (6d2p.pdb1.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 6D2P
  • CSU: Contacts of Structural Units for 6D2P
  • Structure Factors (459 Kb)
  • Retrieve 6D2P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D2P from S2C, [Save to disk]
  • View 6D2P 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 6D2P
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d2p_L] [6d2p_C] [6d2p_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6D2P
  • Community annotation for 6D2P at PDBWiki (http://pdbwiki.org)

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