1T9S

Catalytic Domain Of Human Phosphodiesterase 5A in Complex with GMP

Structural Biology Knowledgebase: 1T9S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1T9S

Classification: HYDROLASE

Total Structure Weight: 80730.05

Macromolecule Entities
Molecule Chains Length Organism Details
cGMP-specific 3',5'-cyclic phosphodiesterase A, B 347 Homo sapiens EC#: 3.1.4.35 IUBMB
Fragment: CATALYTIC DOMAIN
Mutation: R658P, N661S, S663Q, Y664F, I665L, Q576I, R667N, S668T, E669N, H670S, P671E, Q674L, L675M, C676AN, H678E, I680V, M681L
Gene Name(s): PDE5A Gene View PDE5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-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)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.175
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.97 α = 90.00
b = 90.87 β = 98.07
c = 68.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-18
  • Released Date: 2004-08-03
  • Deposition author(s): Zhang, K.Y.J., Card, G.L., Suzuki, Y., Artis, D.R., Fong, D., Gillette, S., Hsieh, D., Neiman, J., West, B.L., Zhang, C., Milburn, M.V., Kim, S.-H., Schlessinger, J., Bollag, G.

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