1T64

Crystal Structure of human HDAC8 complexed with Trichostatin A

Structural Biology Knowledgebase: 1T64 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1T64

Classification: hydrolase

Total Structure Weight: 85198.32

Macromolecule Entities
Molecule Chains Length Organism Details
Histone deacetylase 8 A, B 377 Homo sapiens EC#: 3.5.1.98 IUBMB
Mutation: P31L
Gene Name(s): HDAC8 Gene View HDACL1 CDA07
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B TRICHOSTATIN A
4-HEPTADIENAMIDE,,6- DIMETHYL-7-OXO-2 (Synonym)
C17 H22 N2 O3
RTKIYFITIVXBLE-QEQCGCAPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TSN IC50: 1.38 - 1380 nM (96 - 100) BindingDB
Kd: 390 - 490 nM (100) BindingDB
Ki: 130 nM (100) BindingDB
ΔG: -36 kJ/mol (100) BindingDB
ΔH: -49 - -36.9 kJ/mol (100) BindingDB
-TΔS: 0.1 - 1.1 kJ/mol (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.172
  • Space Group: P 43
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.01 α = 90.00
b = 81.01 β = 90.00
c = 114.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-05
  • Released Date: 2004-07-27
  • Deposition author(s): Somoza, J.R., Skene, R.J., Katz, B.A., Mol, C., Ho, J.D., Jennings, A.J., Luong, C., Arvai, A., Buggy, J.J., Chi, E., Tang, J., Sang, B.-C., Verner, E., Wynands, R., Leahy, E.M., Dougan, D.R., Snell, G., Navre, M., Knuth, M.W., Swanson, R.V., McRee, D.E., Tari, L.W.

Revision History

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