1JED

Crystal Structure of ATP Sulfurylase in complex with ADP

Structural Biology Knowledgebase: 1JED SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 1JED

Classification: TRANSFERASE

Total Structure Weight: 119173.10

Macromolecule Entities
Molecule Chains Length Organism Details
SULFATE ADENYLYLTRANSFERASE A, B 510 Saccharomyces cerevisiae EC#: 2.7.7.4 IUBMB
Gene Name(s): MET3 YJR010W J1436
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A, B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A, B 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A, B ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

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

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

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.192
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 186.13 α = 90.00
b = 186.13 β = 90.00
c = 223.25 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-06-17
  • Released Date: 2001-11-14
  • Deposition author(s): Ullrich, T.C., Huber, R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values