4NCO Viral Protein Immune System date Oct 24, 2013
title Crystal Structure Of The Bg505 Sosip Gp140 Hiv-1 Env Trimer With The Broadly Neutralizing Fab Pgt122
authors J.P.Julien, R.L.Stanfield, D.Lyumkis, A.B.Ward, I.A.Wilson
compound source
Molecule: Bg505 Sosip Gp120
Chain: A, E, I
Fragment: Unp Residues 30-504
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Env
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek

Molecule: Bg505 Sosip Gp41
Chain: B, F, J
Fragment: See Remark 999
Engineered: Yes

Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Env
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek

Molecule: Pgt122 Light Chain
Chain: C, G, K
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: Hek

Molecule: Pgt122 Heavy Chain
Chain: D, H, L
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: Hek
symmetry Space Group: C 1 2 1
R_factor 0.375 R_Free 0.389
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.200 260.720 283.180 90.00 99.56 90.00
method X-Ray Diffractionresolution 4.70 Å
ligand BMA, MAN, NAG enzyme
note 4NCO (Molecule of the Month:pdb170)
Gene
Ontology
ChainFunctionProcessComponent
A, I, E


Primary referenceCrystal Structure of a Soluble Cleaved HIV-1 Envelope Trimer., Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA, Science. 2013 Oct 31. PMID:24179159
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (908 Kb) [Save to disk]
  • Biological Unit Coordinates (4nco.pdb1.gz) 884 Kb
  • LPC: Ligand-Protein Contacts for 4NCO
  • CSU: Contacts of Structural Units for 4NCO
  • Structure Factors (763 Kb)
  • Retrieve 4NCO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NCO from S2C, [Save to disk]
  • Re-refined 4nco structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NCO 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 4NCO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4NCO, from MSDmotif at EBI
  • Fold representative 4nco from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nco_K] [4nco_A] [4nco_B] [4nco_I] [4nco_G] [4nco_C] [4nco_H] [4nco_D] [4nco] [4nco_L] [4nco_E] [4nco_F] [4nco_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4NCO: [IG_like] [IGv ] by SMART
  • Other resources with information on 4NCO
  • Community annotation for 4NCO at PDBWiki (http://pdbwiki.org)

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