5GQQ Apoptosis date Aug 08, 2016
title Structure Of Alg-2hebp2 Complex
authors X.Liu, J.Ma, H.Zhang, Y.Feng
compound source
Molecule: Heme-Binding Protein 2
Chain: A, B
Fragment: Unp Residues 20-197
Synonym: Placental Protein 23,Pp23,Protein Soul
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hebp2, C6orf34, Soul
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_strain: Bl21-Gold(De3)Plyss Ag

Molecule: Programmed Cell Death Protein 6
Chain: C, D
Fragment: Unp Residues 24-191
Synonym: Apoptosis-Linked Gene 2 Protein,Probable Calcium-B Protein Alg-2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdcd6, Alg2
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_strain: Bl21-Gold(De3)Plyss Ag
symmetry Space Group: P 1
R_factor 0.194 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.279 78.124 87.171 113.71 105.64 93.95
method X-Ray Diffractionresolution 2.20 Å
ligand CA, CL enzyme
Gene
Ontology
ChainFunctionProcessComponent
D, C


Primary referenceStructural and Functional Study of Apoptosis-linked Gene-2.Heme-binding Protein 2 Interactions in HIV-1 Production., Ma J, Zhang X, Feng Y, Zhang H, Wang X, Zheng Y, Qiao W, Liu X, J Biol Chem. 2016 Dec 23;291(52):26670-26685. doi: 10.1074/jbc.M116.752444. Epub , 2016 Oct 26. PMID:27784779
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]
  • Biological Unit Coordinates (5gqq.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 5GQQ
  • CSU: Contacts of Structural Units for 5GQQ
  • Structure Factors (643 Kb)
  • Retrieve 5GQQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GQQ from S2C, [Save to disk]
  • Re-refined 5gqq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GQQ 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 5GQQ
  • 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
  • Fold representative 5gqq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gqq] [5gqq_C] [5gqq_B] [5gqq_A] [5gqq_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5GQQ: [EFh ] by SMART
  • Other resources with information on 5GQQ
  • Community annotation for 5GQQ at PDBWiki (http://pdbwiki.org)

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