SAXSdb — 5jqs

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

Protein FAM63A

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 110–384	Not recorded	Ubiquitin-40S ribosomal protein S27a × 1 （P62992） AYE prop-2-en-1-amine × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1 DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；100mM MES, 10% Dioxane and 1.6 M ammonium sulphate	Resolution 2.65 Å R-free 0.231

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 5JQS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JKN Crystal structure of deubiquitinase MINDY-1 Deposited 2016-04-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–384（275 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 PO4 PHOSPHATE ION × 1 HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；100mM Hepes-Na pH 7.5, 200mM NaCl and 25% PEG4000	Resolution 3.00 Å R-free 0.242
5MN9 Crystal structure of MINDY-1 tMIU in complex with K48-diUb Deposited 2016-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 388–426（39 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293.15 K；100 mM sodium acetate pH 5.4 and 18.5 % PEG3350	Resolution 2.05 Å R-free 0.223
6TUV Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin Deposited 2020-01-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 110–384（275 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400	Resolution 2.16 Å R-free 0.249
6TXB Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin Deposited 2020-01-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 110–384（275 aa）	Mutation：C137A, P138A	NA SODIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2 M Sodium malonate, 20% PEG 3350	Resolution 2.18 Å R-free 0.246
6Y6R Crystal structure of MINDY1 T335D mutant Deposited 2020-02-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–384（275 aa）	Mutation：T335D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium pH 7.5, 0.8 M Potassium sodium tartrate tetrahydrate	Resolution 3.32 Å R-free 0.243
6Z90 Crystal structure of MINDY1 mutant-P138A Deposited 2020-06-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–384（275 aa）	Mutation：P138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.7 M sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane pH 7.0	Resolution 3.59 Å R-free 0.258

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

View Construct and Data Evidence

UniProt name	FA63A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–289； UniProt 110–384

Ubiquitin-40S ribosomal protein S27a

Bos taurus

UniProt P62992

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 D； UniProt 1–76	Not recorded	Protein FAM63A × 1 （Q8N5J2） AYE prop-2-en-1-amine × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1 DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；100mM MES, 10% Dioxane and 1.6 M ammonium sulphate	Resolution 2.65 Å R-free 0.231

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 5JQS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4M0W Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin Deposited 2013-08-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；295 K；18% PEG 3000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.40 Å R-free 0.180
4Y1H Crystal structure of K33 linked tri-Ubiquitin Deposited 2015-02-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100mM Bis Tris propane (pH 7.5), 20mM sodium/potassium phosphate, 20% PEG3350	Resolution 1.40 Å R-free 0.194
4Z9S Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin Deposited 2015-04-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–76（76 aa） Fragment：UNP RESIDUES 1-76 Chain B 1–76（76 aa） Fragment：UNP RESIDUES 1-76 Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76 Chain D 1–76（76 aa） Fragment：UNP RESIDUES 1-76	Not recorded	MLA MALONIC ACID × 6 SCN THIOCYANATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4；292 K；3.4M SODIUM MALONATE, 0.1 M SODIUM THIOSUCCINATE PH4.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K	Resolution 2.30 Å R-free 0.223
5BZ0 Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin Deposited 2015-06-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 10,000.	Resolution 2.10 Å R-free 0.228
5FER Complex of TRIM25 RING with UbcH5-Ub Deposited 2015-12-17	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 C 1–76（76 aa） Chain F 1–76（76 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；10% PEG 20000 and 100 mM Tris pH 8.5	Resolution 2.34 Å R-free 0.273
5MN9 Crystal structure of MINDY-1 tMIU in complex with K48-diUb Deposited 2016-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293.15 K；100 mM sodium acetate pH 5.4 and 18.5 % PEG3350	Resolution 2.05 Å R-free 0.223
5XU8 Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine Deposited 2017-06-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：UNP residues 1-76	Not recorded	DX4 2-amino-1,9-dihydro-6H-purine-6-thione × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 5 NA SODIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；24.5% PEG3350, 0.2 M MgC12, 0.1 M Bis-Tris	Resolution 1.81 Å R-free 0.238
5XVE Crystal structure of human USP2 C276S mutant in complex with ubiquitin Deposited 2017-06-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：UNP residues 1-76	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；21% PEG3350, 8% Tacsimate (pH8.0)	Resolution 1.24 Å R-free 0.164
6DJW Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex Deposited 2018-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–74（74 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1 M Tris-HCl, pH 8.0, 15% w/v PEG2000 MME, 0.1 M potasssium chloride	Resolution 3.80 Å R-free 0.297
6DJX Crystal Structure of pParkin-pUb-UbcH7 complex Deposited 2018-05-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M HEPES, pH 6.5, 6% isopropanol, 50 mM magnesium chloride, 5% w/v PEG4000	Resolution 4.80 Å R-free 0.290
6E2B Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3) Deposited 2018-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–76（76 aa） Chain C 1–76（76 aa） Chain E 1–76（76 aa） Chain G 1–76（76 aa） Chain I 1–76（76 aa） Chain P 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 8 PT7 chloro[2-(pyridin-2-yl-kappaN)phenyl-kappaC~1~](triphenyl-lambda~5~-phosphanyl)platinum(2+) × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；3M ammonium sulfate, 0.1M sodium citrate buffer, pH 5.5	Resolution 1.45 Å R-free 0.207
6Q01 TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2 Deposited 2019-08-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 2 BEZ BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20 mM TRIS pH 7.5, 100 mM NaCl, 150 mM Magnesium Formate, 200 mM Potassium Formate, 18% (w/v) PEG 3350	Resolution 0.85 Å R-free 0.114
6Q01 TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2 Deposited 2019-08-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20 mM TRIS pH 7.5, 100 mM NaCl, 150 mM Magnesium Formate, 200 mM Potassium Formate, 18% (w/v) PEG 3350	Resolution 0.85 Å R-free 0.114
7F0U porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono ubiquitin Deposited 2021-06-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；19% PEG-3350, 50 mM HEPES pH 8.0 and 1% w/v tryptone	Resolution 2.20 Å R-free 0.260
7F0U porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono ubiquitin Deposited 2021-06-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；19% PEG-3350, 50 mM HEPES pH 8.0 and 1% w/v tryptone	Resolution 2.20 Å R-free 0.260
7NWH Mammalian pre-termination 80S ribosome with eRF1 and eRF3 bound by Blasticidin S. Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain ff 83–150（68 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 281 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 BLS BLASTICIDIN S × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50 mM HEPES pH 7.4 100 mM KOAc 5 mM Mg(Oac)2 1mM DTT cryo-EM vitrification conditions Cryogen ETHANE；30s sample incubation on grid followed by 1.1s blotting time.	Resolution 4.10 Å

14 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RS27A_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–76； UniProt 1–76

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	5jqs
Deposition date deposition_date	2016-05-05
Structure title title	Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin
Keywords keywords	Hydrolase, Cysteine protease, isopeptidase and Ubiquitin binding; HYDROLASE
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	23.07 Å
Radius of gyration Rg (electron density) rg_electron	22.07 Å
Forward intensity I(0) i0	22066200.00
Molecular weight molecular_weight	36074.0 kDa
Excluded volume excluded_volume	45274 Å³
Envelope volume envelope_volume	55515 Å³
Hydration-shell volume shell_volume	21517 Å³
Envelope diameter envelope_diameter	74.2 Å
Shell Rg shell_rg	28.41 Å
Envelope Rg envelope_rg	22.20 Å
Shape Rg shape_rg	22.07 Å
Total Rg total_rg	22.95 Å
Total atoms total_atoms	2535
Residues n_residues	326
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	73.8 Å
Rg (real space) rg_real	23.05 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.2070e+07
I(0) uncertainty (real space) i0_real_error	3.1650e+05
Rg (reciprocal space) rg_reciprocal	23.06 Å
I(0) (reciprocal space) i0_reciprocal	22070000.0000
Solution quality estimate total_estimate	0.9032
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.307
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5832000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Protein FAM63A
Molecular weight formula_weight	32038.2 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	3157

GPLGSPEFPGRLEMEPDFYCVKWIPWKGEQTPIITQSTNGPCPLLAIMNILFLQWKVKLPPQKEVITSDELMAHLGNCLLSIKPQEKSEGLQLNFQQNVDDAMTVLPKLATGLDVNVRFTGVSDFEYTPECSVFDLLGIPLYHGWLVDPQSPEAVRAVGKLSYNQLVERIITCKHSSDTNLVTEGLIAEQFLETTAAQLTYHGLCELTAAAKEGELSVFFRNNHFSTMTKHKSHLYLLVTDQGFLQEEQVVWESLHNVDGDSCFCDSDFHLSHSLGKGPGAEGGSGSPE

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	Ubiquitin-40S ribosomal protein S27a
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Bos taurus

Entity 3 Entity 3 non-polymer

Description description	prop-2-en-1-amine
Molecular weight formula_weight	57.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5jqsd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

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8. Citations (1)

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Unit-cell length a length_a	82.336 Å
Unit-cell length b length_b	82.336 Å
Unit-cell length c length_c	332.464 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 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	48.630 Å
R factor r_factor	0.2067
R_work r_work	0.2053
R_free r_free	0.2309

fit	/app/data/saxs_computation/jq/5jqs/5jqs.fit
pddf	/app/data/pr_computation/jq/5jqs/5jqs.pr.out
profile	/app/data/saxs_computation/jq/5jqs/5jqs.dat

Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin

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

Protein FAM63A

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-40S ribosomal protein S27a

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 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)