1PK8

Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP

Structural Biology Knowledgebase: 1PK8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 1PK8

Classification: MEMBRANE PROTEIN

Total Structure Weight: 368821.19

Macromolecule Entities
Molecule Chains Length Organism Details
rat synapsin I A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 422 Rattus norvegicus Fragment: A, B & C domains
Gene Name(s): Syn1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F, G, H ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

A, B, C, D, E, F, G, H CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ATP N/A in BindingDB
Kd: 120 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.222
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.60 α = 80.60
b = 78.40 β = 76.90
c = 135.00 γ = 71.80

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-05
  • Released Date: 2004-03-23
  • Deposition author(s): Brautigam, C.A., Chelliah, Y., Deisenhofer, J.

Revision History

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