3AXM

Structure of rice Rubisco in complex with 6PG

Structural Biology Knowledgebase: 3AXM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3AXM

Classification: Lyase

Total Structure Weight: 546188.34

Macromolecule Entities
Molecule Chains Length Organism Details
Ribulose bisphosphate carboxylase large chain A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 477 Oryza sativa EC#: 4.1.1.39 IUBMB
Gene Name(s): rbcL LOC_Osp1g00420 Nip064
Ribulose bisphosphate carboxylase small chain, chloroplastic S, T, U..., V, W, X, Y, ZS, T, U, V, W, X, Y, Z 129 Oryza sativa EC#: 4.1.1.39 IUBMB
Gene Name(s): RBCS RBCS-C Os12g0274700 LOC_Os12g17600 OsJ_016909

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6PG
Query on 6PG

A, B, C, D, E, F, G, H 6-PHOSPHOGLUCONIC ACID
C6 H13 O10 P
BIRSGZKFKXLSJQ-SQOUGZDYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F, G, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
6PG N/A in BindingDB
Ki: 8500 nM  BindingMOAD
Ki: 8500 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B, C, D, E, F, G, H L-PEPTIDE LINKING C7 H14 N2 O4 LYS
NME
Query on NME
S, T, U, V, W, X, Y, Z NON-POLYMER C H5 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.171
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.41 α = 90.00
b = 199.62 β = 91.45
c = 111.17 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