6VDK Transferase Dna date Dec 27, 2019
title Cryoem Structure Of Hiv-1 Conserved Intasome Core
authors M.Li, X.Chen, R.Craigie
compound source
Molecule: Integrase
Chain: A, B, C, D, I, J, M, P
Ec: 2.7.7.-
Engineered: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_common: Hiv-1
Organism_taxid: 11676
Gene: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (27-Mer)
Chain: E, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Dna (25-Mer)
Chain: F, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 1
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.50 Å
ligand DLU, MG enzyme Transferase E.C.2.7.7 BRENDA
A, J, P, B, M, C, D, I

Primary referenceA Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies., Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie R, J Mol Biol. 2020 Feb 13. pii: S0022-2836(20)30106-6. doi:, 10.1016/j.jmb.2020.01.040. PMID:32061936
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (236 Kb) [Save to disk]
  • Biological Unit Coordinates (6vdk.pdb1.gz) 221 Kb
  • LPC: Ligand-Protein Contacts for 6VDK
  • CSU: Contacts of Structural Units for 6VDK
  • Retrieve 6VDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VDK from S2C, [Save to disk]
  • View 6VDK 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 6VDK
  • 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
  • Fold representative 6vdk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vdk_M] [6vdk_B] [6vdk_I] [6vdk_J] [6vdk_P] [6vdk_G] [6vdk_F] [6vdk_D] [6vdk_A] [6vdk_H] [6vdk_C] [6vdk_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VDK
  • Community annotation for 6VDK at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science