2D1S

Crystal structure of the thermostable Japanese Firefly Luciferase complexed with High-energy intermediate analogue

Structural Biology Knowledgebase: 2D1S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2D1S

Classification: Oxidoreductase

Total Structure Weight: 60795.31

Macromolecule Entities
Molecule Chains Length Organism Details
Luciferin 4-monooxygenase A 548 Luciola cruciata EC#: 1.13.12.7 IUBMB
Mutation: C64X, T217I
Gene Name(s):

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

A 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
C21 H18 N8 O8 S3
LJLYTUYNVSHXQB-SOONXTGKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.180
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.59 α = 90.00
b = 181.31 β = 90.00
c = 52.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-08-31
  • Released Date: 2006-03-21
  • Deposition author(s): Nakatsu, T., Ichiyama, S., Hiratake, J., Saldanha, A., Kobashi, N., Sakata, K., Kato, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

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