1E6J Viral Protein date Aug 18, 2000
title Crystal Structure Of Hiv-1 Capsid Protein (P24) In Complex W Fab13b5
authors C.Berthet-Colominas, S.Monaco, A.Novelli, G.Sibai, F.Mallet, S.Cu
compound source
Molecule: Immunoglobulin
Chain: H
Fragment: Heavy Chain 1-219
Other_details: Obtained By Papain Cleavage (Fab)
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Immunoglobulin
Chain: L
Fragment: Light Chain 1-210
Other_details: Obtained By Papain Cleavage (Fab)

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Capsid Protein P24
Chain: P
Fragment: Gag Polyprotein Residues 143-352
Synonym: Ca
Engineered: Yes
Other_details: His6 Tag At N-Term, Pro1 And Ile2 Deleted, C Modified

Organism_scientific: Hiv-1 M\:B_hxb2r
Organism_taxid: 11706
Variant: Clone 12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: See Reference 2
symmetry Space Group: C 1 2 1
R_factor 0.210 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
193.080 45.600 132.470 90.00 132.41 90.00
method X-Ray Diffractionresolution 3.00 Å
note 1E6J (Molecule of the Month:pdb163)
related structures by homologous chain: 1A43, 1ACY, 1AE6, 1BMX, 1GWP, 3CK0

Primary referenceMutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24., Monaco-Malbet S, Berthet-Colominas C, Novelli A, Battai N, Piga N, Cheynet V, Mallet F, Cusack S, Structure. 2000 Oct 15;8(10):1069-77. PMID:11080628
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (1e6j.pdb1.gz) 103 Kb
  • CSU: Contacts of Structural Units for 1E6J
  • Likely Quarternary Molecular Structure file(s) for 1E6J
  • Structure Factors (109 Kb)
  • Retrieve 1E6J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1E6J from S2C, [Save to disk]
  • Re-refined 1e6j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1E6J 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 1E6J
  • 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 1E6J, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1e6jh1, region H:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1e6jh2, region H:121-219 [Jmol] [rasmolscript] [script source]
        - Domain d1e6jl1, region L:1-105 [Jmol] [rasmolscript] [script source]
        - Domain d1e6jl2, region L:106-210 [Jmol] [rasmolscript] [script source]
        - Domain d1e6jp2, region P:11-147 [Jmol] [rasmolscript] [script source]
        - Domain d1e6jp1, region P:148-220 [Jmol] [rasmolscript] [script source]
  • Fold representative 1e6j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1e6j_L] [1e6j_P] [1e6j_H] [1e6j]
  • SWISS-PROT database: [P04585] [Q99LC4]
  • Domain organization of [POL_HV1H2] [Q99LC4_MOUSE] by SWISSPFAM
  • Domains found in 1E6J: [IG_like] [IGv ] by SMART
  • Other resources with information on 1E6J
  • Community annotation for 1E6J 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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