2JIG

CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII PROLYL-4 HYDROXYLASE TYPE I COMPLEXED WITH ZINC AND PYRIDINE-2,4-DICARBOXYLATE

Structural Biology Knowledgebase: 2JIG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2JIG

Classification: HYDROLASE

Total Structure Weight: 50535.39

Macromolecule Entities
Molecule Chains Length Organism Details
PROLYL-4 HYDROXYLASE A, B 224 Chlamydomonas reinhardtii Details: N-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM G30

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PD2
Query on PD2

A PYRIDINE-2,4-DICARBOXYLIC ACID
C7 H5 N O4
MJIVRKPEXXHNJT-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)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PD2 N/A in BindingDB
Ki: 70000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.183
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.92 α = 90.00
b = 60.25 β = 90.00
c = 116.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-06-28
  • Released Date: 2007-10-30
  • Deposition author(s): Koski, M.K., Hieta, R., Bollner, C., Kivirikko, K.I., Myllyharju, J., Wierenga, R.K.

Revision History

  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor