← Back to search

Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：O00571 New Search
17PDB entries
27Biological assembly
31chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2I4I Crystal Structure of human DEAD-box RNA helicase DDX3X Deposited 2006-08-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 167–581（415 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；1.75M Na formate, 0.1M Tris pH 7.5, 20mM ATPgS and MgCl2, VAPOR DIFFUSION, temperature 277K
Resolution 2.20 Å R-free 0.218
2JGN DDX3 helicase domain Deposited 2007-02-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 408–579（172 aa） Fragment：HELICASE DOMAIN, RESIDUES 408-579
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.
Resolution 1.91 Å R-free 0.255
2JGN DDX3 helicase domain Deposited 2007-02-13 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 408–579（172 aa） Fragment：HELICASE DOMAIN, RESIDUES 408-579
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.
Resolution 1.91 Å R-free 0.255
2JGN DDX3 helicase domain Deposited 2007-02-13 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 408–579（172 aa） Fragment：HELICASE DOMAIN, RESIDUES 408-579
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.
Resolution 1.91 Å R-free 0.255
3JRV Structure of poxvirus K7 protein in complex with RNA helicase DDX3 Deposited 2009-09-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 71–90（20 aa） Fragment：DDX3, UNP residues 71-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；100mM sodium citrate, 15.0% (w/v) PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.60 Å R-free 0.190
3JRV Structure of poxvirus K7 protein in complex with RNA helicase DDX3 Deposited 2009-09-09 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 71–90（20 aa） Fragment：DDX3, UNP residues 71-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；100mM sodium citrate, 15.0% (w/v) PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.60 Å R-free 0.190
3JRV Structure of poxvirus K7 protein in complex with RNA helicase DDX3 Deposited 2009-09-09 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain E 71–90（20 aa） Fragment：DDX3, UNP residues 71-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；100mM sodium citrate, 15.0% (w/v) PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.60 Å R-free 0.190
4O2C An Nt-acetylated peptide complexed with HLA-B*3901 Deposited 2013-12-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 17% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.202
4O2E A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 2–10（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.98 Å R-free 0.208
4O2E A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain F 2–10（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.98 Å R-free 0.208
4O2F A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 3–10（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2M sodium formate, 20% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.213
4O2F A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain F 3–10（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2M sodium formate, 20% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.213
4PX9 DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop Deposited 2014-03-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 135–407（273 aa） Fragment：UNP residues 135-407
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.31 Å R-free 0.285
4PX9 DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop Deposited 2014-03-22 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 135–407（273 aa） Fragment：UNP residues 135-407
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.31 Å R-free 0.285
4PX9 DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop Deposited 2014-03-22 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 135–407（273 aa） Fragment：UNP residues 135-407
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.31 Å R-free 0.285
4PXA DEAD-box RNA helicase DDX3X Cancer-associated mutant D354V Deposited 2014-03-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 135–582（448 aa） Fragment：D1-D2, UNP residues 135-582
Mutation：D354V ADP ADENOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.66 M NaH2PO4 0.24 M K2HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 3.20 Å R-free 0.271
5E7I Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 Deposited 2015-10-12 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 133–584（452 aa） Fragment：DEAD-box domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3350, sodium citrate
Resolution 2.22 Å R-free 0.259
5E7I Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 Deposited 2015-10-12 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 133–584（452 aa） Fragment：DEAD-box domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3350, sodium citrate
Resolution 2.22 Å R-free 0.259
5E7I Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 Deposited 2015-10-12 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 133–584（452 aa） Fragment：DEAD-box domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3350, sodium citrate
Resolution 2.22 Å R-free 0.259
5E7J Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMP Deposited 2015-10-12 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 133–584（452 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate
Resolution 2.23 Å R-free 0.264
5E7M Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMPPNP Deposited 2015-10-12 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 133–584（452 aa） Fragment：DEAD-box domains
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG-3000, sodium citrate
Resolution 2.30 Å R-free 0.284
6CZ5 Crystal structure of small molecule AMP-acrylamide covalently bound to DDX3 S228C Deposited 2018-04-08 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 132–607（476 aa） Fragment：UNP residues 132-607
Mutation：S228C FPJ 5'-O-[(R)-hydroxy(propanoylamino)phosphoryl]adenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；100 mM sodium citrate, 8% PEG3000
Resolution 3.00 Å R-free 0.267
6O5F Crystal structure of DEAD-box RNA helicase DDX3X at pre-unwound state Deposited 2019-03-02 Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 132–607（476 aa）
Chain B 132–607（476 aa）
Not recorded CL CHLORIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；25% (v/v) PEG 3350, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5
Resolution 2.50 Å R-free 0.246
7LIU DDX3X bound to ATP analog and remodeled RNA:DNA hybrid Deposited 2021-01-27 Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 135–582（448 aa）
Chain B 135–582（448 aa）
Not recorded MG MAGNESIUM ION × 2 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M HEPEs pH 7.5, 16% PEG 3350, 0.1 M Li3Citrate, 0.1 M Na3Citrate, 2% benzamidine-HCl, 5 mM ADP-BeF3
Resolution 3.00 Å R-free 0.241
7YMF Crystal Structure of DDX3X449_450ET>DP Deposited 2022-07-28 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 133–414（282 aa）
Chain B 415–584（170 aa）
Mutation：E449D, T450P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES pH 6.5, 1.5 M Sodium Formate , 50 mM Magnesium chloride
Resolution 2.30 Å R-free 0.244
8SSW Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state Deposited 2023-05-09 Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 132–607（476 aa）
Chain B 132–607（476 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG3350, Magnesium Chloride, etc.
Resolution 2.40 Å R-free 0.248
9E2C Crystal structure of DEAD-box RNA helicase DDX3X R326H mutant Deposited 2024-10-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 115–591（477 aa）
Mutation：R326H GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；0.1 M Bis-Tris pH 5.5, 25% PEG3350, 0.2 M Lithium sulfate, 0.01 M Strontium(II) chloride
Resolution 2.30 Å R-free 0.244

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.