8TBX | pdb_00008tbx

Crystal structure of human DDX1 helicase in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb8TBX/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-06-29 Released: 2023-07-26 
• Deposition Author(s): Zeng, H., Dong, A., Li, Y., Yen, H., Hejazi, Z., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.286 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of human DDX1 helicase in complex with ADP

Zeng, H., Dong, A., Li, Y., Yen, H., Hejazi, Z., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.91 kDa 
• Atom Count: 3,476 
• Modeled Residue Count: 458 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX1	A	470	Homo sapiens	Mutation(s): 0  Gene Names: DDX1 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q92499 (Homo sapiens) Explore Q92499  Go to UniProtKB:  Q92499
PHAROS:  Q92499 GTEx:  ENSG00000079785

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.286 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38TBX

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.708	α = 90
b = 71.517	β = 90
c = 138.496	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Zeng, H., Dong, A., Li, Y., Yen, H., Hejazi, Z., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	U54 AG065187

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Author supporting evidence, Data collection