6KQD Transcription date Aug 17, 2019
title Thermus Thermophilus Initial Transcription Complex Comprisin And 5'-Oh Rna Of 3 Nt
authors Y.Zhang, L.Li, R.H.Ebright
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, K, L
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, M
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, N
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, O
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F, P
Engineered: Yes

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Siga, Ttha0532
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna (5'- D(Cpcptgpcpaptpcpcpgptpgpapgptpcpcpapgp
Chain: G, Q
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Tpaptpapaptpgpgpgpapgpcptpgptpcpapcpgp Gpcpapgpg)-3');
Chain: H, R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R(Gpgpa)-3')
Chain: I, S
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.207 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
185.501 104.044 297.441 90.00 98.50 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand DG, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


F, P
  • bacterial sigma factor activ...


  • M, C


    N, D


    O, E


    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1171 Kb) [Save to disk]
  • Biological Unit Coordinates (6kqd.pdb1.gz) 591 Kb
  • Biological Unit Coordinates (6kqd.pdb2.gz) 589 Kb
  • LPC: Ligand-Protein Contacts for 6KQD
  • CSU: Contacts of Structural Units for 6KQD
  • Structure Factors (1471 Kb)
  • Retrieve 6KQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6KQD from S2C, [Save to disk]
  • View 6KQD 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 6KQD
  • 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 6kqd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6kqd_R] [6kqd_S] [6kqd_G] [6kqd_M] [6kqd_P] [6kqd_D] [6kqd_B] [6kqd_O] [6kqd_F] [6kqd_I] [6kqd_A] [6kqd_L] [6kqd_Q] [6kqd_H] [6kqd_E] [6kqd_N] [6kqd_K] [6kqd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6KQD
  • Community annotation for 6KQD at PDBWiki (http://pdbwiki.org)

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