3IKH | pdb_00003ikh

Crystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb3IKH/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-05 Released: 2009-08-18 
• Deposition Author(s): Satyanarayana, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.240 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae

Satyanarayana, L., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.43 kDa 
• Atom Count: 9,000 
• Modeled Residue Count: 1,140 
• Deposited Residue Count: 1,196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbohydrate kinase	A, B, C, D	299	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN78578_16990, KPN78578_16990/5340552, KPN_01729 EC: 2.7.1.15
UniProt
Find proteins for A6T989 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T989  Go to UniProtKB:  A6T989

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], F [auth B], G [auth C], I [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL	H [auth C], J [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.240 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.332	α = 90
b = 106.352	β = 99.51
c = 122.056	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Satyanarayana, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-27
  Changes: Structure summary