4IMY Transferase date Jan 03, 2013
title The Aff4 Scaffold Binds Human P-Tefb Adjacent To Hiv Tat
authors T.Alber, U.Schulze-Gahmen
compound source
Molecule: Cyclin-Dependent Kinase 9
Chain: A, C, E
Fragment: 1-330
Synonym: C-2k, Cell Division Cycle 2-Like Protein Kinase 4, Division Protein Kinase 9, Serinethreonine-Protein Kinase Tat-Associated Kinase Complex Catalytic Subunit;
Ec: 2.7.11.22, 2.7.11.23
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdk9, Cdc2l4, Tak
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Cyclin-T1
Chain: B, D, F
Fragment: 1-264
Synonym: Cyct1, Cyclin-T
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ccnt1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Af4fmr2 Family Member 4
Chain: G, H, I
Fragment: 2-73
Synonym: All1-Fused Gene From Chromosome 5q31 Protein, Prot 5q31, Major Cdk9 Elongation Factor-Associated Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aff4, Af5q31, Mcef, Hspc092
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.691 126.298 195.626 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.94 Å
ligand AMP, TPO enzyme Transferase E.C.2.7.11.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, E


Primary referenceThe AFF4 scaffold binds human P-TEFb adjacent to HIV Tat., Schulze-Gahmen U, Upton H, Birnberg A, Bao K, Chou S, Krogan NJ, Zhou Q, Alber T, Elife. 2013;2:e00327. doi: 10.7554/eLife.00327. Epub 2013 Mar 5. PMID:23471103
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (939 Kb) [Save to disk]
  • Biological Unit Coordinates (4imy.pdb1.gz) 308 Kb
  • Biological Unit Coordinates (4imy.pdb2.gz) 319 Kb
  • Biological Unit Coordinates (4imy.pdb3.gz) 308 Kb
  • LPC: Ligand-Protein Contacts for 4IMY
  • CSU: Contacts of Structural Units for 4IMY
  • Structure Factors (366 Kb)
  • Retrieve 4IMY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IMY from S2C, [Save to disk]
  • Re-refined 4imy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IMY 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 4IMY
  • 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 4IMY, from MSDmotif at EBI
  • Fold representative 4imy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4imy_H] [4imy_D] [4imy_I] [4imy_F] [4imy_B] [4imy_A] [4imy_G] [4imy] [4imy_E] [4imy_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4IMY: [CYCLIN] [S_TKc ] by SMART
  • Other resources with information on 4IMY
  • Community annotation for 4IMY at PDBWiki (http://pdbwiki.org)

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