6D2P Crystal structure of IOMA-class CLK31 Fab from an HIV-1 naive donor in complex with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.6 A date
authors Sarkar, A., Wilson, I.A.
compound source
symmetry
R_factor
R_Free 0.2676
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.60
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] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (6d2p.pdb1.gz) 94 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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