2ZT6 | pdb_00002zt6

Crystal structure of human Glycyl-tRNA synthetase (GlyRS) in complex with AMPCPP

PDB DOI: https://doi.org/10.2210/pdb2ZT6/pdb

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

Deposited: 2008-09-19 Released: 2009-08-25
Deposition Author(s): Guo, R.T., Yang, X.L., Schimmel, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.08 Å
R-Value Free:
0.244 (Depositor), 0.245 (DCC)
R-Value Work:
0.225 (Depositor), 0.226 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis

Guo, R.T., Chong, Y.E., Guo, M., Yang, X.L.

To be published.

Macromolecule Content

Total Structure Weight: 79.21 kDa
Atom Count: 4,373
Modeled Residue Count: 530
Deposited Residue Count: 693
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycyl-tRNA synthetase	A	693	Homo sapiens	Mutation(s): 0 Gene Names: GARS EC: 6.1.1.14 (PDB Primary Data), 2.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P41250 (Homo sapiens) Explore P41250 Go to UniProtKB: P41250
PHAROS: P41250 GTEx: ENSG00000106105
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41250
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC Query on APC Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.08 Å
R-Value Free: 0.244 (Depositor), 0.245 (DCC)
R-Value Work: 0.225 (Depositor), 0.226 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.608	α = 90
b = 138.862	β = 90
c = 133.819	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-08-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
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.