2H59

Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose

Structural Biology Knowledgebase: 2H59 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 2H59

Classification: Hydrolase

Total Structure Weight: 60494.25

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent deacetylase A, B 246 Thermotoga maritima EC#: 3.5.1 IUBMB
Mutation: H116A
Gene Name(s): cobB sir2 TM_0490
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cellular tumor antigen p53 D, E 18 Homo sapiens Gene Name(s): TP53 Gene View P53
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B (2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)- 5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN- 2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)- 4,5-DIHYDROXYTETRAHYDROFURAN-3-YL ACETATE
C17 H25 N5 O15 P2
HNHCIVXQBMBKPQ-ARMUENPQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
APR
Query on APR

A ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.205
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.00 α = 90.00
b = 47.00 β = 90.00
c = 257.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-05-25
  • Released Date: 2006-09-05
  • Deposition author(s): Hoff, K.G., Avalos, J.L., Sens, K., Wolberger, C.

Revision History

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