SAXSdb — 6gzj

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

Dynein light chain 1, cytoplasmic

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–89	Not recorded	Myelin-associated glycoprotein × 1 （P20917） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate, and 25% (w/v) PEG 3350	Resolution 1.98 Å R-free 0.229

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 6GZJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMI STRUCTURE OF THE HUMAN PIN/LC8 DIMER WITH A BOUND PEPTIDE Deposited 1999-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–89（85 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；pH 8.4	Resolution 2.50 Å R-free 0.283
1CMI STRUCTURE OF THE HUMAN PIN/LC8 DIMER WITH A BOUND PEPTIDE Deposited 1999-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 5–89（85 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；pH 8.4	Resolution 2.50 Å R-free 0.283
3ZKE Structure of LC8 in complex with Nek9 peptide Deposited 2013-01-22	Different construct Different mutation/modification Different oligomeric state 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） Chain C 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.228
3ZKE Structure of LC8 in complex with Nek9 peptide Deposited 2013-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–89（89 aa） Chain G 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.228
3ZKE Structure of LC8 in complex with Nek9 peptide Deposited 2013-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–89（89 aa） Chain K 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.228
3ZKF Structure of LC8 in complex with Nek9 phosphopeptide Deposited 2013-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–89（89 aa） Chain K 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.269
3ZKF Structure of LC8 in complex with Nek9 phosphopeptide Deposited 2013-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–89（89 aa） Chain C 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.269
3ZKF Structure of LC8 in complex with Nek9 phosphopeptide Deposited 2013-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–89（89 aa） Chain I 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.269
6GZL Complex between the dynein light chain DYNLL1/DLC8 and a peptide from the large myelin-associated glycoprotein L-MAG Deposited 2018-07-04	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–89（89 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate, and 25% (w/v) PEG 3350	Resolution 1.95 Å R-free 0.251
6RLB Structure of the dynein-2 complex; tail domain Deposited 2019-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–89（89 aa） Chain J 1–89（89 aa） Chain K 1–89（89 aa） Chain L 1–89（89 aa） Chain M 1–89（89 aa） Chain N 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6SC2 Structure of the dynein-2 complex; IFT-train bound model Deposited 2019-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–89（89 aa） Chain J 1–89（89 aa） Chain K 1–89（89 aa） Chain L 1–89（89 aa） Chain M 1–89（89 aa） Chain N 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7D35 Human LC8 bound to ebola virus VP35(67-76) Deposited 2020-09-18	Different oligomeric state 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	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200mM ammonium citrate dibasic, 200mM ammonium citrate tribasic (pH 5.5), 30% (w/v) polyethylene glycol 3350	Resolution 2.40 Å R-free 0.292
8PR0 Cytoplasmic dynein-A heavy chain bound to dynactin-p150glued and IC-LC tower Deposited 2023-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain E 1–89（89 aa） Chain F 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.40 Å
8PR1 Cytoplasmic dynein-B heavy chain bound to IC-LC tower Deposited 2023-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain D 1–89（89 aa） Chain E 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
8PTK Composite structure of Dynein-Dynactin-JIP3-LIS1 Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 53 PDB declaration: 53-meric	Chain a 1–89（89 aa） Chain b 1–89（89 aa） Chain d 1–89（89 aa） Chain i 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 16 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ZN ZINC ION × 3 MG MAGNESIUM ION × 6 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.00 Å
8RGG Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy chain DYNC2H1. Deposited 2023-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain I 1–89（89 aa） Chain J 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9BLY Composite structure of full-length human dynein-1 in phi-particle conformation Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain I 1–89（89 aa） Chain J 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 5 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9E12 Full-length human dynein-1 in phi comformation under Lis1 condition Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–89（89 aa） Chain J 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9E13 Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–89（89 aa） Chain J 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9E14 Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain I 1–89（89 aa） Chain J 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.00 Å
9E23 Cryo-EM structure of Pre-Chi dynein tail Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain d 1–89（89 aa） Chain i 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.20 Å
9E28 Cryo-EM structure of Phi dynein tail Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain d 1–89（89 aa） Chain i 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
9NZ7 Crystal structure of human DYNLL1-S64A/S88A mutant dimer Deposited 2025-03-31	Different construct Different mutation/modification 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） Chain B 1–89（89 aa）	Mutation：S64A, S88A Mutation：S64A, S88A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；24% PEG2000 MME, 50 mM calcium chloride, 100 mM HEPES, 10 mM DTT, 10% glycerol	Resolution 1.41 Å R-free 0.234
9NZ7 Crystal structure of human DYNLL1-S64A/S88A mutant dimer Deposited 2025-03-31	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–89（89 aa）	Mutation：S64A, S88A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；24% PEG2000 MME, 50 mM calcium chloride, 100 mM HEPES, 10 mM DTT, 10% glycerol	Resolution 1.41 Å R-free 0.234
9YNE Motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain d 1–89（89 aa） Chain i 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.46 Å
9YNH Full-length human cytoplasmic dynein-1 in phi-like state bound to dynactin-p150glued and LIS1 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain I 1–89（89 aa） Chain J 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.50 Å

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

View Construct and Data Evidence

UniProt name	DYL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 1–89

Myelin-associated glycoprotein

OrganismNot specified

UniProt P20917

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 573–626	Not recorded	Dynein light chain 1, cytoplasmic × 1 （P63167） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate, and 25% (w/v) PEG 3350	Resolution 1.98 Å R-free 0.229

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 6GZJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5LF5 Myelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with co-purified ligand Deposited 2016-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–508（489 aa）	Not recorded	MAN alpha-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；100 mM NaCl, 20 mM Tris/HCl pH 7.0, 7.7 % PEG 4000 (w/v)	Resolution 3.80 Å R-free 0.228
5LFR Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 Deposited 2016-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–325（306 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol	Resolution 2.12 Å R-free 0.262
5LFR Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 Deposited 2016-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–325（306 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol	Resolution 2.12 Å R-free 0.262
5LFU Myelin-associated glycoprotein (MAG) glycosylated and lysine-methylated full extracellular domain Deposited 2016-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–508（489 aa）	Not recorded	MAN alpha-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Crystals were grown from protein that was modified by reductive lysine methylation. Protein was concentrated to 8.4 mg/mL, which was mixed 1:1 with reservoir solution. Crystals grew in a condition containing 200 mM NaOAc and 20 % PEG3350 (w/v).	Resolution 4.30 Å R-free 0.295
5LFV Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand Deposited 2016-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–325（306 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol	Resolution 2.30 Å R-free 0.254
5LFV Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand Deposited 2016-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–325（306 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol	Resolution 2.30 Å R-free 0.254

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAG_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–54； UniProt 573–626

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	6gzj
Deposition date deposition_date	2018-07-04
Structure title title	Complex between the dynein light chain DYNLL1/DLC8 and the specific domain of large myelin-associated glycoprotein L-MAG
Keywords keywords	complex, heterotetramer, cell adhesion, cytoplasmic domain, PROTEIN BINDING; PROTEIN BINDING
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	14.01 Å
Radius of gyration Rg (electron density) rg_electron	12.56 Å
Forward intensity I(0) i0	2707240.00
Molecular weight molecular_weight	11406.0 kDa
Excluded volume excluded_volume	14268 Å³
Envelope volume envelope_volume	15661 Å³
Hydration-shell volume shell_volume	10575 Å³
Envelope diameter envelope_diameter	42.1 Å
Shell Rg shell_rg	18.38 Å
Envelope Rg envelope_rg	12.98 Å
Shape Rg shape_rg	12.52 Å
Total Rg total_rg	14.01 Å
Total atoms total_atoms	801
Residues n_residues	98
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	43.8 Å
Rg (real space) rg_real	13.91 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.7070e+06
I(0) uncertainty (real space) i0_real_error	3.1720e+04
Rg (reciprocal space) rg_reciprocal	13.92 Å
I(0) (reciprocal space) i0_reciprocal	2707000.0000
Solution quality estimate total_estimate	0.8884
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.2 Å
Skewness Skewness skewness	0.117
Kurtosis Kurtosis kurtosis	-0.371
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	611000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.914

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Dynein light chain 1, cytoplasmic
Molecular weight formula_weight	10469.0 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	816

SMCDRKAVIKNADMSEEMQQDSVECATQALEKYNIEKDIAAHIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Myelin-associated glycoprotein
Molecular weight formula_weight	6191.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SEKRLGSERRLLGLRGESPELDLSYSHSDLGKRPTKDSYTLTEELAEYAEIRVK

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6gzjA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily	10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

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8. Citations (1)

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Unit-cell length a length_a	44.050 Å
Unit-cell length b length_b	44.050 Å
Unit-cell length c length_c	204.460 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	1.977 Å
Low-resolution limit resolution_low	38.148 Å
R factor r_factor	0.1931
R_work r_work	0.1915
R_free r_free	0.2289

fit	/app/data/saxs_computation/gz/6gzj/6gzj.fit
pddf	/app/data/pr_computation/gz/6gzj/6gzj.pr.out
profile	/app/data/saxs_computation/gz/6gzj/6gzj.dat

Complex between the dynein light chain DYNLL1/DLC8 and the specific domain of large myelin-associated glycoprotein L-MAG

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

Myelin-associated glycoprotein

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)