5BYF | pdb_00005byf

Crystal structure of human ribokinase in complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb5BYF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-10 Released: 2016-06-15 
• Deposition Author(s): Park, J., Chakrabarti, J., Singh, B., Gupta, R.S., Junop, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human ribokinase in complex with AMP

Park, J., Chakrabarti, J., Singh, B., Gupta, R.S., Junop, M.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)

Macromolecule Content 

• Total Structure Weight: 71.3 kDa 
• Atom Count: 4,987 
• Modeled Residue Count: 625 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B	330	Homo sapiens	Mutation(s): 0  Gene Names: RBKS, RBSK EC: 2.7.1.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H477 (Homo sapiens) Explore Q9H477  Go to UniProtKB:  Q9H477
PHAROS:  Q9H477 GTEx:  ENSG00000171174

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
CL	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A], G [auth B], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.09	α = 90
b = 63.87	β = 90
c = 181.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Park, J., Chakrabarti, J., Singh, B., Gupta, R.S., Junop, M.S.

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description