2B63

Complete RNA Polymerase II-RNA inhibitor complex

Structural Biology Knowledgebase: 2B63 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.252

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2B63

Classification: TRANsferase / RNA

Total Structure Weight: 525031.65


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase II largest subunit A 1733 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
DNA-directed RNA polymerase II 140 kDa polypeptide B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
DNA-directed RNA polymerase II 45 kDa polypeptide C 318 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB3 YIL021W
DNA-directed RNA polymerase II 32 kDa polypeptide D 221 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB4 YJL140W J0654
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide E 215 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB5 RPA7 RPC9 YBR154C YBR1204
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide F 155 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
DNA-directed RNA polymerase II 19 kDa polypeptide G 171 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB7 YDR404C D9509.22
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide H 146 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB8 YOR224C YOR50-14
DNA-directed RNA polymerase II subunit 9 I 122 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB9 YGL070C
DNA-directed RNA polymerases I/II/III subunit 10 J 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB10 YOR210W
DNA-directed RNA polymerase II 13.6 kDa polypeptide K 120 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB11 YOL005C
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide L 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
Macromolecule Entities
Molecule Chains Length Organism Details
31-MER R 31 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A, B, C, I, J, L ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5BU
Query on 5BU
R RNA LINKING C9 H12 Br N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.252
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 224.59 α = 90.00
b = 399.82 β = 90.00
c = 286.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-09-30
  • Released Date: 2005-12-06
  • Deposition author(s): Kettenberger, H., Eisenfuehr, A., Brueckner, F., Theis, M., Famulok, M., Cramer, P.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4