2GK6

Structural and Functional insights into the human Upf1 helicase core

Structural Biology Knowledgebase: 2GK6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.235

Literature

Macromolecules
Sequence Display for 2GK6

Classification: HYDROLASE

Total Structure Weight: 141207.09

Macromolecule Entities
Molecule Chains Length Organism Details
Regulator of nonsense transcripts 1 A, B 624 Homo sapiens EC#: 3.6.4 IUBMB
Fragment: helicase core domain(residues 295-914)
Gene Name(s): UPF1 Gene View KIAA0221 RENT1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 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)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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: 2.4 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.235
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.28 α = 114.41
b = 67.84 β = 90.13
c = 87.25 γ = 110.22

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-31
  • Released Date: 2007-01-09
  • Deposition author(s): Cheng, Z., Muhlrad, D., Parker, R., Song, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor