1RBZ | pdb_00001rbz

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

PDB DOI: https://doi.org/10.2210/pdb1RBZ/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:
0.270 (Depositor), 0.261 (DCC)
R-Value Work:
0.245 (Depositor), 0.236 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Human GAR Tfase complex structure

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

To be published.

Macromolecule Content

Total Structure Weight: 47.48 kDa
Atom Count: 3,288
Modeled Residue Count: 400
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE	A, B	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22102
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KT5 Query on KT5 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N-{4-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDRO-PYRIMIDIN-5-YL)-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXY-ETHYL)-BUT-2-YL-BENZOYL}-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GLUTAMIC ACID C₄₂ H₅₄ F₃ N₉ O₂₀ IWEGOVKIJZGOSL-RCZRCYCLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.270 (Depositor), 0.261 (DCC)
R-Value Work: 0.245 (Depositor), 0.236 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.157	α = 90
b = 126.157	β = 90
c = 93.987	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-06-14

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.