2QBY

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.226

Literature

Macromolecules
Sequence Display for 2QBY

Classification: REPLICATION / DNA

Total Structure Weight: 108917.64


Macromolecule Entities
Molecule Chains Length Organism Details
Cell division control protein 6 homolog 1 A 386 Sulfolobus solfataricus Fragment: Residues 15-397
Gene Name(s): cdc6-1 SSO0257
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cell division control protein 6 homolog 3 B 384 Sulfolobus solfataricus Fragment: Residues 14-394
Gene Name(s): cdc6-3 SSO2184
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (33-MER) C 33 synthetic
DNA (33-MER) D 33 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A, B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SPD
Query on SPD

C SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) (Synonym)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.226
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 77.65 α = 90.00
b = 199.14 β = 90.00
c = 213.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-06-18
  • Released Date: 2007-09-11
  • Deposition author(s): Cunningham Dueber, E.L., Corn, J.E., Bell, S.D., Berger, J.M.

Revision History

  • 2011-07-13
    Type: Version format compliance