5OT2

RNA polymerase II elongation complex in the presence of 3d-Napht-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 5OT2

Classification: TRANSCRIPTION

Total Structure Weight: 530696.00


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase II subunit RPB1 A 1733 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB2 B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB3 C 318 Saccharomyces cerevisiae Gene Name(s): RPB3 YIL021W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB4 D 221 Saccharomyces cerevisiae Gene Name(s): RPB4 YJL140W J0654
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC1 E 215 Saccharomyces cerevisiae Gene Name(s): RPB5 RPA7 RPC9 YBR154C YBR1204
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC2 F 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB7 G 171 Saccharomyces cerevisiae Gene Name(s): RPB7 YDR404C D9509.22
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC3 H 146 Saccharomyces cerevisiae Gene Name(s): RPB8 YOR224C YOR50-14
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB9 I 122 Saccharomyces cerevisiae Gene Name(s): RPB9 YGL070C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC5 J 70 Saccharomyces cerevisiae Gene Name(s): RPB10 YOR210W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB11 K 120 Saccharomyces cerevisiae Gene Name(s): RPB11 YOL005C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC4 L 70 Saccharomyces cerevisiae Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA template strand T 26 Synthetic construct
DNA non-template strand N 14 Synthetic construct
RNA product strand P 11 Synthetic construct

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

T 2-ethyl-7-methoxy-naphthalene
C13 H14 O
IZQPFGFFOUIMRX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, I, J, L ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
4DU
Query on 4DU
T DNA LINKING C11 H15 N4 O6 P --
BRU
Query on BRU
T DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.178
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 221.35 α = 90.00
b = 394.93 β = 90.00
c = 283.71 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-08-19
  • Released Date: 2017-11-01
  • Deposition author(s): Malvezzi, S., Farnung, L., Aloisi, C., Angelov, T., Cramer, P., Sturla, S.J.

Revision History

  • Version 1_0: 2017-11-01

    Type: Initial release

  • Version 1_1: 2017-11-15

    Type: Database references