3AXK

Structure of rice Rubisco in complex with NADP(H)

Structural Biology Knowledgebase: 3AXK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3AXK

Classification: Lyase

Total Structure Weight: 137833.89

Macromolecule Entities
Molecule Chains Length Organism Details
Ribulose bisphosphate carboxylase large chain A, B 477 Oryza sativa EC#: 4.1.1.39 IUBMB
Gene Name(s): rbcL LOC_Osp1g00420 Nip064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ribulose bisphosphate carboxylase small chain, chloroplastic S, T 129 Oryza sativa EC#: 4.1.1.39 IUBMB
Mutation: L112C
Gene Name(s): RBCS RBCS-C Os12g0274700 LOC_Os12g17600 OsJ_016909
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NDP N/A in BindingDB
Ki: 70000 nM  BindingMOAD
Ki: 70000 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B L-PEPTIDE LINKING C7 H14 N2 O4 LYS
NME
Query on NME
S, T NON-POLYMER C H5 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.169
  • Space Group: I 4
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.25 α = 90.00
b = 110.25 β = 90.00
c = 199.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-11
  • Released Date: 2012-04-11
  • Deposition author(s): Matsumura, H., Mizohata, E., Ishida, H., Kogami, A., Ueno, T., Makino, A., Inoue, T., Yokota, A., Mae, T., Kai, Y.

Revision History

  • 2013-06-05
    Type: Citation | Details: Citation update
  • 2012-06-13
    Type: Citation | Details: Citation update