8SSW | pdb_00008ssw

Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state

PDB DOI: https://doi.org/10.2210/pdb8SSW/pdb
NAKB: 8SSW

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-09 Released: 2024-05-22
Deposition Author(s): Song, H., Ji, X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.248 (Depositor), 0.240 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state

Song, H., Ji, X.

To be published.

Macromolecule Content

Total Structure Weight: 126.58 kDa
Atom Count: 8,280
Modeled Residue Count: 918
Deposited Residue Count: 1,008
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX3X	A, B	476	Homo sapiens	Mutation(s): 0 Gene Names: DDX3X, DBX, DDX3 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens) Explore O00571 Go to UniProtKB: O00571
PHAROS: O00571 GTEx: ENSG00000215301
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00571
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (28-MER)	C, D	28	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain H [auth C] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C]	H [auth C], J [auth D], K [auth D], L [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]