1IKJ

1.27 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEXED WITH IMIDAZOLE

Structural Biology Knowledgebase: 1IKJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.127

Literature

Macromolecules
Sequence Display for 1IKJ

Classification: TRANSPORT PROTEIN

Total Structure Weight: 20978.40

Macromolecule Entities
Molecule Chains Length Organism Details
NITROPHORIN 4 A 184 Rhodnius prolixus EC#: 1.7.6.1 IUBMB
Details: IMIDAZOLE OCCUPIES THE FE SIXTH COORDINATION POSITION THE HEME IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS. THE ONLY EVIDENCE OF THIS DISORDER IS THE APPEARANCE OF METHYL GROUPS CMB AND CMC AS VINYLS. THESE EXTRA ATOMS ARE CALLED CBBB AND CBCB. THE LOOP CONTAINING RESIDUES 125-130 IS DISORDERED. IT HAS BEEN BUILT IN TWO POSITIONS, BUT THIS MODEL DOES NOT COMPLETELY EXPLAIN THE ELECTRON DENSITY.
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.127
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.18 α = 90.00
b = 42.48 β = 94.28
c = 52.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-05-03
  • Released Date: 2001-10-03
  • Deposition author(s): Roberts, S.A., Weichsel, A., Qui, Y., Shelnutt, J.A., Walker, F.A., Montfort, W.R.

Revision History

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