1RBY | pdb_00001rby

Human GAR Tfase complex structure with 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid and substrate beta-GAR

• PDB DOI: https://doi.org/10.2210/pdb1RBY/pdb

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


• Deposited: 2003-11-03 Released: 2005-06-14 
• Deposition Author(s): Zhang, Y., Desharnais, J., Boger, D.L., Wilson, I.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Human GAR Tfase complex structure

Zhang, Y., Desharnais, J., Boger, D.L., Wilson, I.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 93.48 kDa 
• Atom Count: 6,727 
• Modeled Residue Count: 800 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE	A, B, C, D	209	Homo sapiens	Mutation(s): 0  Gene Names: purN EC: 2.1.2.2 (PDB Primary Data), 6.3.4.13 (UniProt), 6.3.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P22102 (Homo sapiens) Explore P22102  Go to UniProtKB:  P22102
PHAROS:  P22102 GTEx:  ENSG00000159131

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KEU	E [auth A], G [auth B], I [auth C], J [auth D]	N-{4-[(1R)-4-[(2R,4R,5S)-2,4-DIAMINO-6-OXOHEXAHYDROPYRIMIDIN-5-YL]-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXYETHYL)BUTYL]BENZOYL}-D-GLUTAMIC ACID C22 H30 F3 N5 O8 KOLDLUFBEMUZIM-YNPGLMGXSA-N
GAR	F [auth A], H [auth B]	GLYCINAMIDE RIBONUCLEOTIDE C7 H13 N2 O8 P OBQMLSFOUZUIOB-SHUUEZRQSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.171	α = 90
b = 126.171	β = 90
c = 95.389	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Zhang, Y., Desharnais, J., Boger, D.L., Wilson, I.A.

Revision History  

• Version 1.0: 2005-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary