4XEM

Crystal Structure of wild type human AlaRS catalytic domain

PDB DOI: https://doi.org/10.2210/pdb4XEM/pdb

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

Deposited: 2014-12-24 Released: 2016-02-17
Deposition Author(s): Zhou, H., He, W., Yang, X.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.179
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of wild type human AlaRS catalytic domain

Zhou, H., Yang, X.L.

To be published.

Macromolecule Content

Total Structure Weight: 54.04 kDa
Atom Count: 3,595
Modelled Residue Count: 377
Deposited Residue Count: 475
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine--tRNA ligase, cytoplasmic	A	475	Homo sapiens	Mutation(s): 0 Gene Names: AARS EC: 6.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P49588 (Homo sapiens) Explore P49588 Go to UniProtKB: P49588
PHAROS: P49588 GTEx: ENSG00000090861
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49588
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A5A Query on A5A Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE C₁₃ H₁₉ N₇ O₇ S CWWYMWDIYBJVLP-YTMOPEAISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.179
R-Value Work: 0.161
R-Value Observed: 0.162
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.121	α = 90
b = 67.131	β = 127.42
c = 75.107	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Zhou, H.

He, W.

Yang, X.L.

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4XEM

Crystal Structure of wild type human AlaRS catalytic domain

Crystal structure of wild type human AlaRS catalytic domain

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)