5jsg

Crystal structure of Spindlin1 bound to compound EML405

Method: X-RAY DIFFRACTION D_max: 103.5 Å Quality: GOOD

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

Spindlin-1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 50–262	Fragment：Spin/Ssty Repeats, UNP residues 50-262	6P9 [2-(phenylamino)-1,4-phenylene]bis({4-[2-(pyrrolidin-1-yl)ethyl]piperidin-1-yl}methanone) × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 20% PEG 10000	Resolution 2.50 Å R-free 0.245
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 50–262	Fragment：Spin/Ssty Repeats, UNP residues 50-262	6P9 [2-(phenylamino)-1,4-phenylene]bis({4-[2-(pyrrolidin-1-yl)ethyl]piperidin-1-yl}methanone) × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 20% PEG 10000	Resolution 2.50 Å R-free 0.245

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 5JSG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NS2 Crystal Structure of Spindlin1 Deposited 2006-11-02	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 26–262（237 aa） Fragment：residues 1-237 (26-262) Chain B 26–262（237 aa） Fragment：residues 1-237 (26-262)	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；Ammonium Sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.20 Å R-free 0.260
4H75 Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide Deposited 2012-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–262（236 aa） Fragment：UNP residues 27-262	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 3 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；289 K；0.1 M CHES, pH 9.5, 2.1 M ammonium sulfate, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.10 Å R-free 0.218
4MZF Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide Deposited 2013-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–262（213 aa） Fragment：UNP residues 50-262	Not recorded	CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.10 Å R-free 0.255
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–262（213 aa） Fragment：UNP residues 50-262	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 1.70 Å R-free 0.207
4MZG Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide Deposited 2013-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 50–262（213 aa） Fragment：UNP residues 50-262	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 1.70 Å R-free 0.207
4MZH Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide Deposited 2013-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 50–262（213 aa） Fragment：UNP residues 50-262	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.20 Å R-free 0.247
5JSJ Crystal structure of Spindlin1 bound to compound EML631 Deposited 2016-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–262（213 aa） Fragment：Spin/Ssty Repeats, UNP residues 50-262	Not recorded	6PD [4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 25% PEG 3350	Resolution 2.35 Å R-free 0.249
5JSJ Crystal structure of Spindlin1 bound to compound EML631 Deposited 2016-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 50–262（213 aa） Fragment：Spin/Ssty Repeats, UNP residues 50-262	Not recorded	6PD [4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2M MgCl2, 0.1M HepesNa, 25% PEG 3350	Resolution 2.35 Å R-free 0.249
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 51–262（212 aa） Fragment：UNP residues 51-262	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris	Resolution 3.30 Å R-free 0.308
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–262（212 aa） Fragment：UNP residues 51-262	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris	Resolution 3.30 Å R-free 0.308
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 51–262（212 aa） Fragment：UNP residues 51-262	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris	Resolution 3.30 Å R-free 0.308
5Y5W Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide Deposited 2017-08-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 51–262（212 aa） Fragment：UNP residues 51-262	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.5 M (NH4)2SO4, 0.1 M Bis-Tris	Resolution 3.30 Å R-free 0.308
6I8B Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn Deposited 2018-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–262（214 aa）	Not recorded	H7T 2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]-1,2,3-triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone × 1 DMS DIMETHYL SULFOXIDE × 4 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；55% MPD and 0.1 M SPG buffer pH 5.5	Resolution 1.76 Å R-free 0.254
6I8B Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn Deposited 2018-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 49–262（214 aa）	Not recorded	H7T 2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]-1,2,3-triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone × 1 DMS DIMETHYL SULFOXIDE × 1 GLY GLYCINE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；55% MPD and 0.1 M SPG buffer pH 5.5	Resolution 1.76 Å R-free 0.254
6I8L Crystal structure of Spindlin1 in complex with the inhibitor TD001851a Deposited 2018-11-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–262（214 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 DMS DIMETHYL SULFOXIDE × 1 H7Q 5'-(cyclopropylmethoxy)-6'-[3-(1,3-dihydroisoindol-2-yl)propoxy]spiro[cyclopentane-1,3'-indole]-2'-amine × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；55% MPD and 0.1 M SPG buffer	Resolution 1.58 Å R-free 0.207
6I8Y Crystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366 Deposited 2018-11-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–262（214 aa）	Not recorded	2OD 5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine × 2 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris pH=6.5,0.2M CaCl2, 45% MPD	Resolution 1.52 Å R-free 0.205
6QPL Crystal structure of Spindlin1 in complex with the inhibitor MS31 Deposited 2019-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–262（214 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 2 JC5 [3-(aminomethyl)-5-[3-(1,3-dihydroisoindol-2-yl)propoxy]-4-methoxy-phenyl]methanamine × 1 GLY GLYCINE × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；60% MPD and 0.1 M SPG buffer pH 6.0	Resolution 1.60 Å R-free 0.208
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0	Resolution 3.10 Å R-free 0.264
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0	Resolution 3.10 Å R-free 0.264
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0	Resolution 3.10 Å R-free 0.264
7BQZ Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide Deposited 2020-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；2.8M sodium acetate, pH7.0	Resolution 3.10 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO	Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO	Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO	Resolution 3.50 Å R-free 0.264
7BU9 Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex Deposited 2020-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 45–262（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；3.6M sodium formate, 3% DMSO	Resolution 3.50 Å R-free 0.264
7CNA Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide Deposited 2020-07-30	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 51–262（212 aa） Chain D 51–262（212 aa）	Not recorded	BEN BENZAMIDINE × 6 CL CHLORIDE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M sodium cacodylate pH 6.5, 35% PEG3350, 5% glycerol, 2% Benzamidine hydrochloride	Resolution 1.60 Å R-free 0.201
7E9M Crystal Structure of Spindlin1 bound to SPINDOC Docpep3 Deposited 2021-03-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–262（262 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.2M magnesium acetate, 0.1M Sodium cacodylate pH 6.5, 20% PEG 8000	Resolution 2.50 Å R-free 0.253
7E9M Crystal Structure of Spindlin1 bound to SPINDOC Docpep3 Deposited 2021-03-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–262（262 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.2M magnesium acetate, 0.1M Sodium cacodylate pH 6.5, 20% PEG 8000	Resolution 2.50 Å R-free 0.253
7EA1 Crystal Structure of Spindlin1 bound to SPINDOC Docpep2 Deposited 2021-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 50–262（213 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.1M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 1.5M Ammonium sulfate	Resolution 2.70 Å R-free 0.286
7EA1 Crystal Structure of Spindlin1 bound to SPINDOC Docpep2 Deposited 2021-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 50–262（213 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.1M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 1.5M Ammonium sulfate	Resolution 2.70 Å R-free 0.286
7OCB Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B Deposited 2021-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–262（214 aa）	Not recorded	V88 7-[3-(1,3-dihydroisoindol-2-yl)propoxy]-2N-[2-(dimethylamino)ethyl]-6-methoxy-4N-(1-propan-2-ylpiperidin-4-yl)quinazoline-2,4-diamine × 1 PO4 PHOSPHATE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CL CHLORIDE ION × 1 GLY GLYCINE × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；55-60 % MPD and 0.1 M SPG buffer pH 5.5-6.0	Resolution 1.42 Å R-free 0.206
8GTX Crystal Structure of human Spindlin1-HBx complex Deposited 2022-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 50–262（213 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；16%(w/v) PEG 8000, 0.04M Potassium phosphate dibasic, 20% (v/v) Glycerol	Resolution 1.80 Å R-free 0.197
9T2Z Spindlin 1 with crystallization epitope mutations H127D:L128D:T131R Deposited 2025-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–262（214 aa）	Mutation：H127D:L128D:T131R	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.2M ammonium sulfate 25% PEG3350 0.1M HEPES pH 7.5	Resolution 1.87 Å R-free 0.288

19 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPIN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–222； UniProt 50–262 Author chain B； PDBConstruct 10–222； UniProt 50–262

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5jsg
Deposition date deposition_date	2016-05-08
Structure title title	Crystal structure of Spindlin1 bound to compound EML405
Keywords keywords	SH3-like, beta barrel, CELL CYCLE; CELL CYCLE
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	28.73 Å
Radius of gyration Rg (electron density) rg_electron	27.93 Å
Forward intensity I(0) i0	33728000.00
Molecular weight molecular_weight	45840.0 kDa
Excluded volume excluded_volume	57727 Å³
Envelope volume envelope_volume	77549 Å³
Hydration-shell volume shell_volume	24581 Å³
Envelope diameter envelope_diameter	107.6 Å
Shell Rg shell_rg	32.99 Å
Envelope Rg envelope_rg	28.01 Å
Shape Rg shape_rg	27.92 Å
Total Rg total_rg	28.55 Å
Total atoms total_atoms	3230
Residues n_residues	388
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	103.5 Å
Rg (real space) rg_real	28.94 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	3.3730e+07
I(0) uncertainty (real space) i0_real_error	5.5050e+05
Rg (reciprocal space) rg_reciprocal	28.85 Å
I(0) (reciprocal space) i0_reciprocal	33730000.0000
Solution quality estimate total_estimate	0.8129
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.530
Kurtosis Kurtosis kurtosis	-0.277
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5898000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.608; Smooth: 0.905

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Spindlin-1
Molecular weight formula_weight	25509.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3343

MHHHHHHGSRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	[2-(phenylamino)-1,4-phenylene]bis({4-[2-(pyrrolidin-1-yl)ethyl]piperidin-1-yl}methanone)
Molecular weight formula_weight	585.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5jsgA00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	70 — Spindlin/Ssty

Domain ID domain_id	5jsgB00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	70 — Spindlin/Ssty

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8. Citations (1)

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Unit-cell length a length_a	43.060 Å
Unit-cell length b length_b	123.908 Å
Unit-cell length c length_c	49.779 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	38.786 Å
R factor r_factor	0.1920
R_work r_work	0.1860
R_free r_free	0.2449

fit	/app/data/saxs_computation/js/5jsg/5jsg.fit
pddf	/app/data/pr_computation/js/5jsg/5jsg.pr.out
profile	/app/data/saxs_computation/js/5jsg/5jsg.dat