4KBE

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with benzoguanamine

Structural Biology Knowledgebase: 4KBE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.157

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KBE

Classification: TRANSFERASE

Total Structure Weight: 79156.59

Macromolecule Entities
Molecule Chains Length Organism Details
Probable sugar kinase protein A, B 352 Rhizobium etli Gene Name(s): RHE_CH00135
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BZE
Query on BZE

A, B 6-phenyl-1,3,5-triazine-2,4-diamine
BENZOGUANAMINE (Synonym)
C9 H9 N5
GZVHEAJQGPRDLQ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A, B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.157
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.07 α = 90.00
b = 90.86 β = 90.00
c = 92.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-23
  • Released Date: 2013-05-22
  • Deposition author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

No revisions since initial release