6VCD Ligase date Dec 20, 2019
title Cryo-Em Structure Of Irp2-Fbxl5-Skp1 Complex
authors H.Wang, H.Shi, N.Zheng
compound source
Molecule: Iron-Responsive Element Binding Protein 2, Isofor
Chain: A
Synonym: Irp2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ireb2, Hcg_38938
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: F-Boxlrr-Repeat Protein 5
Chain: B
Fragment: Unp Residues 183-674
Synonym: Fbxl5,F-Box And Leucine-Rich Repeat Protein 5,F-Bo Fbl4fbl5,P45skp2-Like Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fbxl5, Fbl4, Fbl5, Flr1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: S-Phase Kinase-Associated Protein 1
Chain: C
Synonym: Skp1,Cyclin-Acdk2-Associated Protein P19,P19a,Org Corti Protein 2,Ocp-2,Organ Of Corti Protein II,Ocp-II,Rna II Elongation Factor-Like Protein,Siii,Transcription Elonga Factor B Polypeptide 1-Like,P19skp1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Skp1, Emc19, Ocp2, Skp1a, Tceb1l
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
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 3.00 Å
ligand FES enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


C


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (6vcd.pdb1.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 6VCD
  • CSU: Contacts of Structural Units for 6VCD
  • Retrieve 6VCD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VCD from S2C, [Save to disk]
  • View 6VCD 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 6VCD
  • 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 6vcd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vcd_C] [6vcd_A] [6vcd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VCD
  • Community annotation for 6VCD at PDBWiki (http://pdbwiki.org)

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