5y5w

Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide

Method: X-RAY DIFFRACTION D_max: 107.2 Å Quality: REASONABLE

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 51–262	Fragment：UNP residues 51-262	Histone peptide H4K20(me3) × 1	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 51–262	Fragment：UNP residues 51-262	Histone peptide H4K20(me3) × 1	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 51–262	Fragment：UNP residues 51-262	Histone peptide H4K20(me3) × 1	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 51–262	Fragment：UNP residues 51-262	No other associated polymer	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

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 5Y5W	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 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 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 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 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 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
5JSG Crystal structure of Spindlin1 bound to compound EML405 Deposited 2016-05-08	Different construct 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	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
5JSG Crystal structure of Spindlin1 bound to compound EML405 Deposited 2016-05-08	Different construct 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	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
5JSJ Crystal structure of Spindlin1 bound to compound EML631 Deposited 2016-05-08	Different construct 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 construct 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
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 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 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 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 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 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 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 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 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 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 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 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 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 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 31 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 24–235； UniProt 51–262 Author chain B； PDBConstruct 24–235； UniProt 51–262 Author chain C； PDBConstruct 24–235； UniProt 51–262 Author chain D； PDBConstruct 24–235； UniProt 51–262

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	5y5w
Deposition date deposition_date	2017-08-10
Structure title title	Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide
Keywords keywords	reader, histone, GENE REGULATION; GENE REGULATION
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	34.91 Å
Radius of gyration Rg (electron density) rg_electron	33.55 Å
Forward intensity I(0) i0	126178000.00
Molecular weight molecular_weight	89788.0 kDa
Excluded volume excluded_volume	112290 Å³
Envelope volume envelope_volume	166630 Å³
Hydration-shell volume shell_volume	41041 Å³
Envelope diameter envelope_diameter	119.8 Å
Shell Rg shell_rg	40.71 Å
Envelope Rg envelope_rg	32.91 Å
Shape Rg shape_rg	33.59 Å
Total Rg total_rg	34.03 Å
Total atoms total_atoms	6351
Residues n_residues	819
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	107.2 Å
Rg (real space) rg_real	34.69 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.2620e+08
I(0) uncertainty (real space) i0_real_error	2.0100e+06
Rg (reciprocal space) rg_reciprocal	34.83 Å
I(0) (reciprocal space) i0_reciprocal	126200000.0000
Solution quality estimate total_estimate	0.6014
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	52.4 Å
Skewness Skewness skewness	-0.024
Kurtosis Kurtosis kurtosis	-0.595
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18940000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Spindlin-1
Molecular weight formula_weight	26886.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6354

MSSGHHHHHHHHGSSENLYFQGSRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

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	Histone peptide H4K20(me3)
Molecular weight formula_weight	1212.5 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G

KRHRKVLDN

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5y5wA00
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	5y5wB00
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	5y5wC00
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	5y5wD00
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	88.769 Å
Unit-cell length b length_b	148.504 Å
Unit-cell length c length_c	169.212 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	84.610 Å
R factor r_factor	0.2239
R_work r_work	0.2192
R_free r_free	0.3081

fit	/app/data/saxs_computation/y5/5y5w/5y5w.fit
pddf	/app/data/pr_computation/y5/5y5w/5y5w.pr.out
profile	/app/data/saxs_computation/y5/5y5w/5y5w.dat

Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide

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

Spindlin-1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)