SAXSdb — 7k3k

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dynein light chain 1, cytoplasmic

Drosophila melanogaster

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–89	Not recorded	Protein panoramix × 2 （Q9W2H9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M NH4Ac, 0.1 M Bis-Tris pH 5.5, 17% (w/v) PEG 10000	Resolution 1.42 Å R-free 0.201

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7K3K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RHW The solution structure of the pH-induced monomer of dynein light chain LC8 from Drosophila Deposited 2003-11-14	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–89（89 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；303 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition 0.8-1.4mM LC8 protein \| 50mM citrate phosphate, pH 3.0, 50mM NaCl, 1mM sodium Azide, 10%D20, 3% glycerol	Resolution not provided
2P2T Crystal structure of dynein light chain LC8 bound to residues 123-138 of intermediate chain IC74 Deposited 2007-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa）	Not recorded	ACT ACETATE ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.296
2PG1 Structural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex Deposited 2007-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–89（89 aa） Chain B 1–89（89 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.253
2PG1 Structural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex Deposited 2007-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–89（89 aa） Chain D 1–89（89 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.253
2PG1 Structural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex Deposited 2007-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–89（89 aa） Chain B 1–89（89 aa） Chain C 1–89（89 aa） Chain D 1–89（89 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.253
3BRI Crystal Structure of apo-LC8 Deposited 2007-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–89（89 aa）	Not recorded	ACT ACETATE ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；Potassium tartrate 0.2M, sodium citrate 0.1M, ammonium sulfate 2.0M, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.212
3BRL Crystal Structure of LC8 S88E / Swa Deposited 2007-12-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa）	Mutation：S88E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；Calcium acetate 0.2M, sodium cacodylate 0.1M, 15% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.254
3DVH LC8 Point mutant K36P Deposited 2008-07-18	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–89（89 aa）	Mutation：K36P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM CaCl2, 100 mM HEPES, 28% (w/v) PEG MME 2000, 10% glycerol, 10 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.244
3DVH LC8 Point mutant K36P Deposited 2008-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–89（89 aa） Chain B 1–89（89 aa）	Mutation：K36P Mutation：K36P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM CaCl2, 100 mM HEPES, 28% (w/v) PEG MME 2000, 10% glycerol, 10 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.244
3DVP Pak1 peptide bound LC8 Deposited 2008-07-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa） Chain B 1–89（89 aa）	Mutation：K36P Mutation：K36P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 200 mM NaCl, 27% (w/v) PEG 4000, and 10% 0.1 M (NH4)6CoCl3, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K, temperature 293K	Resolution 2.50 Å R-free 0.263
3DVT Biochemical and structural characterization of the PAK1- LC8 interaction Deposited 2008-07-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–89（89 aa） Chain F 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；50 mM MgCl2, 100 mM MES, 32% (w/v) PEG 4000, and 20% xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.258
3DVT Biochemical and structural characterization of the PAK1- LC8 interaction Deposited 2008-07-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–89（89 aa） Chain D 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；50 mM MgCl2, 100 mM MES, 32% (w/v) PEG 4000, and 20% xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.258
3DVT Biochemical and structural characterization of the PAK1- LC8 interaction Deposited 2008-07-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–89（89 aa） Chain B 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；50 mM MgCl2, 100 mM MES, 32% (w/v) PEG 4000, and 20% xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.258
3E2B Crystal structure of Dynein Light chain LC8 in complex with a peptide derived from Swallow Deposited 2008-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.2M sodium potassium tartrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3FM7 Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; Allosteric Interactions of Dynein Light Chains with Dynein Intermediate Chain Deposited 2008-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–89（89 aa） Chain F 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Hanging Drop；pH 6.5；277.15 K；16% PEG 8K, 100 mM sodium cacodylate, 200 mM calcium acetate, pH 6.5, Hanging Drop, temperature 277.15K	Resolution 3.50 Å R-free 0.275
3GLW Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; Allosteric Interactions of Dynein Light Chains with Dynein Intermediate Chain Deposited 2009-03-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；30% PEG 400, 100 mM Hepes, 200 mM magnesium chloride at pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.15 Å R-free 0.271
4QH7 LC8 - Ana2 (159-168) Complex Deposited 2014-05-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa） Fragment：LC8 Chain B 1–89（89 aa） Fragment：LC8	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.3M magnesium acetate, 0.1M sodium cacodylate, 26% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.83 Å R-free 0.207
4QH7 LC8 - Ana2 (159-168) Complex Deposited 2014-05-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–89（89 aa） Fragment：LC8 Chain F 1–89（89 aa） Fragment：LC8	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.3M magnesium acetate, 0.1M sodium cacodylate, 26% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.83 Å R-free 0.207
4QH8 LC8 - Ana2 (237-246) Complex Deposited 2014-05-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa） Fragment：LC8 Chain B 1–89（89 aa） Fragment：LC8	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；0.19M ammonium acetate, 0.1M sodium acetate, 0.1% beta-mercaptoethanol, and 27% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.90 Å R-free 0.236
4QH8 LC8 - Ana2 (237-246) Complex Deposited 2014-05-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–89（89 aa） Fragment：LC8 Chain F 1–89（89 aa） Fragment：LC8	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；0.19M ammonium acetate, 0.1M sodium acetate, 0.1% beta-mercaptoethanol, and 27% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.90 Å R-free 0.236
4QH8 LC8 - Ana2 (237-246) Complex Deposited 2014-05-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–89（89 aa） Fragment：LC8 Chain H 1–89（89 aa） Fragment：LC8	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；0.19M ammonium acetate, 0.1M sodium acetate, 0.1% beta-mercaptoethanol, and 27% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.90 Å R-free 0.236
5E0L LC8 - Chica (415-424) Complex Deposited 2015-09-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 3–89（87 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M calcium acetate, 0.1 M sodium cacodylate, 15% polyethylene glycol 8000	Resolution 1.31 Å R-free 0.202
5E0M LC8 - Chica (468-476) Complex Deposited 2015-09-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.2 M lithium sulfate, 0.1 M Bis-Tris, 25% polyethylene glycol 3350	Resolution 1.65 Å R-free 0.232
7K3J Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide Deposited 2020-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–89（89 aa） Chain G 1–89（89 aa） Chain I 1–89（89 aa） Chain K 1–89（89 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Li2SO4, 0.1 M Tris pH 8.5, 40% (v/v) PEG 400	Resolution 2.50 Å R-free 0.272
7K3J Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide Deposited 2020-09-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–89（89 aa） Chain E 1–89（89 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Li2SO4, 0.1 M Tris pH 8.5, 40% (v/v) PEG 400	Resolution 2.50 Å R-free 0.272
7K3L Crystal structure of dLC8 in complex with Panoramix TQ peptide Deposited 2020-09-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M KSCN, 30% (w/v) PEG 2000 MME	Resolution 1.79 Å R-free 0.209

17 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DYL1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 1–89

Protein panoramix

Drosophila melanogaster

UniProt Q9W2H9

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 455–467	Fragment：residues 445-467	Dynein light chain 1, cytoplasmic × 2 （Q24117）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M NH4Ac, 0.1 M Bis-Tris pH 5.5, 17% (w/v) PEG 10000	Resolution 1.42 Å R-free 0.201

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7K3K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6IEW The crystal structure of the dNxf2 UBA domain in complex with Panoramix Deposited 2018-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 315–341（27 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；30%(w/v) PEG3350, 0.1M Tris (pH 9.0), 0.2M sodium acetate trihydrate	Resolution 1.50 Å R-free 0.173
6OPF Crystal structure of dmNxf2 UBA domain fused with Panoramix helix Deposited 2019-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 311–340（30 aa） Chain B 311–340（30 aa） Chain D 311–340（30 aa） Chain F 311–340（30 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.095 M Sodium citrate pH 5.6, 19% (v/v) Isopropanol, 19% (w/v) PEG 4000, 5% (v/v) Glycerol	Resolution 2.00 Å R-free 0.246
7K3J Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide Deposited 2020-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 455–480（26 aa） Fragment：residues 455-480 Chain H 455–480（26 aa） Fragment：residues 455-480	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Li2SO4, 0.1 M Tris pH 8.5, 40% (v/v) PEG 400	Resolution 2.50 Å R-free 0.272
7K3J Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide Deposited 2020-09-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 455–480（26 aa） Fragment：residues 455-480 Chain F 455–480（26 aa） Fragment：residues 455-480	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Li2SO4, 0.1 M Tris pH 8.5, 40% (v/v) PEG 400	Resolution 2.50 Å R-free 0.272
7K3L Crystal structure of dLC8 in complex with Panoramix TQ peptide Deposited 2020-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 468–480（13 aa） Fragment：residues 468-480	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M KSCN, 30% (w/v) PEG 2000 MME	Resolution 1.79 Å R-free 0.209
7MKK Crystal structure of Drosophila Panoramix in complex with Sov NTD Deposited 2021-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 83–109（27 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES pH 9.5, 30% (w/v) PEG 3000	Resolution 2.50 Å R-free 0.260
7MKK Crystal structure of Drosophila Panoramix in complex with Sov NTD Deposited 2021-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 83–109（27 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES pH 9.5, 30% (w/v) PEG 3000	Resolution 2.50 Å R-free 0.260
7MKK Crystal structure of Drosophila Panoramix in complex with Sov NTD Deposited 2021-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 83–109（27 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES pH 9.5, 30% (w/v) PEG 3000	Resolution 2.50 Å R-free 0.260
7MKK Crystal structure of Drosophila Panoramix in complex with Sov NTD Deposited 2021-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 83–109（27 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES pH 9.5, 30% (w/v) PEG 3000	Resolution 2.50 Å R-free 0.260

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PANX_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–14； UniProt 455–467

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7k3k
Deposition date deposition_date	2020-09-11
Structure title title	Crystal structure of dLC8 in complex with Panoramix TQT peptide
Keywords keywords	Piwi, transposon silencing, heterochromatin formation, piRNA pathway, transcriptional silencing, RNA BINDING PROTEIN, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.45 Å
Radius of gyration Rg (electron density) rg_electron	13.07 Å
Forward intensity I(0) i0	2898630.00
Molecular weight molecular_weight	11849.0 kDa
Excluded volume excluded_volume	14818 Å³
Envelope volume envelope_volume	16636 Å³
Hydration-shell volume shell_volume	10874 Å³
Envelope diameter envelope_diameter	45.7 Å
Shell Rg shell_rg	18.75 Å
Envelope Rg envelope_rg	13.60 Å
Shape Rg shape_rg	13.04 Å
Total Rg total_rg	14.40 Å
Total atoms total_atoms	835
Residues n_residues	102
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	48.4 Å
Rg (real space) rg_real	14.37 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.8990e+06
I(0) uncertainty (real space) i0_real_error	3.2400e+04
Rg (reciprocal space) rg_reciprocal	14.38 Å
I(0) (reciprocal space) i0_reciprocal	2899000.0000
Solution quality estimate total_estimate	0.6986
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.0 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	689900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.999; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Dynein light chain 1, cytoplasmic
Molecular weight formula_weight	10388.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	986

MSDRKAVIKNADMSEEMQQDAVDCATQALEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETRHFIYFYLGQVAILLFKSG

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Protein panoramix
Molecular weight formula_weight	1641.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

STLYKNAATQTERR

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d7k3ka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.39 — DLC
Superfamily Superfamily superfamily	d.39.1 — DLC
Family Family family	d.39.1.1 — DLC

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8. Citations (1)

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Unit-cell length a length_a	45.639 Å
Unit-cell length b length_b	45.639 Å
Unit-cell length c length_c	202.717 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.415 Å
Low-resolution limit resolution_low	38.794 Å
R factor r_factor	0.1842
R_work r_work	0.1827
R_free r_free	0.2006

fit	/app/data/saxs_computation/k3/7k3k/7k3k.fit
pddf	/app/data/pr_computation/k3/7k3k/7k3k.pr.out
profile	/app/data/saxs_computation/k3/7k3k/7k3k.dat

Crystal structure of dLC8 in complex with Panoramix TQT peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dynein light chain 1, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Protein panoramix

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)