1YDL Transcription date Dec 24, 2004
title Crystal Structure Of The Human Tfiih, Northeast Structural Genomics Target Hr2045.
authors F.Forouhar, W.Edstrom, R.Xiao, T.B.Acton, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg)
compound source
Molecule: General Transcription Factor Iih, Polypeptide 5
Chain: A
Synonym: Tfiih
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: C6orf175
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)+Magic
Expression_system_vector_type: Pet21
Expression_system_plasmid: Bl21
symmetry Space Group: P 21 21 2
R_factor 0.236 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.412 53.922 34.818 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand MSE enzyme
note 1YDL is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (17 Kb) [Save to disk]
  • Biological Unit Coordinates (1ydl.pdb1.gz) 13 Kb
  • LPC: Ligand-Protein Contacts for 1YDL
  • CSU: Contacts of Structural Units for 1YDL
  • Likely Quarternary Molecular Structure file(s) for 1YDL
  • Structure Factors (95 Kb)
  • Retrieve 1YDL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YDL from S2C, [Save to disk]
  • Re-refined 1ydl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YDL 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 1YDL
  • 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 1YDL, from MSDmotif at EBI
  • Fold representative 1ydl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ydl] [1ydl_A]
  • SWISS-PROT database: [Q6ZYL4]
  • Domain organization of [TF2H5_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1YDL with the sequences similar proteins can be viewed for 1YDL's classification [TF2H5_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [TF2H5_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YDL
  • Community annotation for 1YDL 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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