4DO0

Crystal Structure of human PHF8 in complex with Daminozide

Structural Biology Knowledgebase: 4DO0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DO0

Classification: METAL BINDING PROTEIN

Total Structure Weight: 44508.17

Macromolecule Entities
Molecule Chains Length Organism Details
Histone lysine demethylase PHF8 A 374 Homo sapiens EC#: 1.14.11.27 IUBMB
Gene Name(s): PHF8 Gene View KIAA1111 ZNF422
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DZA
Query on DZA

A DAMINOZIDE
C6 H12 N2 O3
NOQGZXFMHARMLW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DZA IC50: 550 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.208
  • Space Group: I 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 151.73 α = 90.00
b = 151.73 β = 90.00
c = 151.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-09
  • Released Date: 2012-03-14
  • Deposition author(s): Krojer, T., Daniel, M., Ng, S.S., Walport, L.J., Chowdhury, R., Arrowsmith, C.H., Edwards, A., Bountra, C., Kawamura, A., Muller-Knapp, S., McDonough, M.A., von Delft, F., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History

No revisions since initial release