6IUX | pdb_00006iux

Crystal structure of a hydrolase protein

PDB DOI: https://doi.org/10.2210/pdb6IUX/pdb

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

Deposited: 2018-12-01 Released: 2019-12-04
Deposition Author(s): Liu, X.H., Yu, X.C.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

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 protein

Liu, X.H., Yu, X.C.

To be published.

Macromolecule Content

Total Structure Weight: 42.56 kDa
Atom Count: 3,290
Modeled Residue Count: 358
Deposited Residue Count: 379
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Protein ADP-ribosylarginine] hydrolase	A	379	Homo sapiens	Mutation(s): 0 Gene Names: ADPRH, ARH1 EC: 3.2.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for P54922 (Homo sapiens) Explore P54922 Go to UniProtKB: P54922
PHAROS: P54922 GTEx: ENSG00000144843
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54922
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 Query on AR6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.159 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.68	α = 90
b = 52.919	β = 90
c = 141.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81672794

Revision History (Full details and data files)

Version 1.0: 2019-12-04
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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.