SAXSdb — 3znz

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

PROTEIN FAM105B

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 80–352	Fragment：OTU DOMAIN, RESIDUES 80-352 Mutation：YES	POLYUBIQUITIN-C × 1 （F5H265） SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；100 MM BIS-TRIS, 2M (NH4)2SO4, PH 6.5	Resolution 1.90 Å R-free 0.222

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 3ZNZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZNV Crystal structure of the OTU domain of OTULIN at 1.3 Angstroms. Deposited 2013-02-18	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 80–352（273 aa） Fragment：OTU DOMAIN, RESIDUES 80-352	Not recorded	GOL GLYCEROL × 4 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100 MM MES/IMIDAZOLE PH 6.5, 30 MM MGCL2, 30 MM CACL2, 10% PEG 4000, 20% GLYCEROL	Resolution 1.30 Å R-free 0.154
3ZNX Crystal structure of the OTU domain of OTULIN D336A mutant Deposited 2013-02-18	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 80–352（273 aa） Fragment：OTU DOMAIN, RESIDUES 80-352	Mutation：YES	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100 MM MES/IMIDAZOLE PH 6.5, 30 MM MGCL2, 30 MM CACL2, 10% PEG 4,000, 20% GLYCEROL	Resolution 1.35 Å R-free 0.159
4KSJ Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom Deposited 2013-05-17	Different construct 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 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Non-standard monomer：Yes (specific site not provided by mmCIF)	BME BETA-MERCAPTOETHANOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；100mM MES, 200mM MgCl2, 19% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.215
4KSK Gumby/Fam105B in complex with ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 55–352（298 aa） Fragment：OTU domain (unp residues 55-352)	Mutation：C129S	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM Bis Tris, 200 mM AmSO4, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.268
4KSK Gumby/Fam105B in complex with ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 55–352（298 aa） Fragment：OTU domain (unp residues 55-352)	Mutation：C129S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM Bis Tris, 200 mM AmSO4, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.268
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 79–352（274 aa） Fragment：OTU domain (unp residues 79-352)	Mutation：C129A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.254
4OYK Structure of HOIP PUB domain bound to OTULIN PIM Deposited 2014-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 49–67（19 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；295 K；32% PEG 6000, 1M LiCl, 100 mM Tris pH 8.4	Resolution 2.00 Å R-free 0.237
4OYK Structure of HOIP PUB domain bound to OTULIN PIM Deposited 2014-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 49–67（19 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；295 K；32% PEG 6000, 1M LiCl, 100 mM Tris pH 8.4	Resolution 2.00 Å R-free 0.237
4P0B Crystal structure of HOIP PUB domain in complex with OTULIN PIM Deposited 2014-02-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 52–61（10 aa） Fragment：UNP Residues 52-61	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 7.5	Resolution 2.70 Å R-free 0.270
4P0B Crystal structure of HOIP PUB domain in complex with OTULIN PIM Deposited 2014-02-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 52–61（10 aa） Fragment：UNP Residues 52-61	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 7.5	Resolution 2.70 Å R-free 0.270
5OE7 Structure of OTULIN bound to the Met1-linked diubiquitin activity probe Deposited 2017-07-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–350（271 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；1.9-2.1 M Ammonium sulphate, 100 mM bis-tris	Resolution 2.95 Å R-free 0.309
6I9C Structure of the OTU domain of OTULIN G281R mutant Deposited 2018-11-22	Different construct 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 80–345（266 aa）	Mutation：G281R	GOL GLYCEROL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；100 mM HEPES pH 7.4, 18 % (w/v) PEG 6,000, 1M LiCl	Resolution 1.77 Å R-free 0.179
6SAK Structure of the OTULINcat C129A - SNX27 PDZ domain complex. Deposited 2019-07-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–352（273 aa）	Mutation：C129A	GOL GLYCEROL × 5 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；291 K；19% (w/v) PEG 3,350, 200 mM Li2(SO4), 100 mM Bis-Tris pH 6.8	Resolution 2.00 Å R-free 0.253
6SAK Structure of the OTULINcat C129A - SNX27 PDZ domain complex. Deposited 2019-07-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 80–352（273 aa）	Mutation：C129A	GOL GLYCEROL × 4 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；291 K；19% (w/v) PEG 3,350, 200 mM Li2(SO4), 100 mM Bis-Tris pH 6.8	Resolution 2.00 Å R-free 0.253
9LZX Crystal structure of the OTU domain of OTULIN in complex with 11B6 Deposited 2025-02-22	Different construct 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 80–345（266 aa）	Not recorded	A1EMF 3-phenyl-5-prop-2-enylsulfanyl-4~{H}-1,2,4-triazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350,MES,magnesium chloride	Resolution 2.00 Å R-free 0.251

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

View Construct and Data Evidence

UniProt name	F105B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–275； UniProt 80–352

POLYUBIQUITIN-C

HOMO SAPIENS

UniProt F5H265

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 1–149	Not recorded	PROTEIN FAM105B × 1 （Q96BN8） SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；100 MM BIS-TRIS, 2M (NH4)2SO4, PH 6.5	Resolution 1.90 Å R-free 0.222

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	F5H265_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–149； UniProt 1–149

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	3znz
Deposition date deposition_date	2013-02-18
Structure title title	Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin
Keywords keywords	HYDROLASE; 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	22.79 Å
Radius of gyration Rg (electron density) rg_electron	21.72 Å
Forward intensity I(0) i0	38437900.00
Molecular weight molecular_weight	47483.0 kDa
Excluded volume excluded_volume	59345 Å³
Envelope volume envelope_volume	68859 Å³
Hydration-shell volume shell_volume	26013 Å³
Envelope diameter envelope_diameter	76.1 Å
Shell Rg shell_rg	28.87 Å
Envelope Rg envelope_rg	21.97 Å
Shape Rg shape_rg	21.70 Å
Total Rg total_rg	22.65 Å
Total atoms total_atoms	3329
Residues n_residues	412
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	73.4 Å
Rg (real space) rg_real	22.67 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	3.8440e+07
I(0) uncertainty (real space) i0_real_error	4.0580e+05
Rg (reciprocal space) rg_reciprocal	22.70 Å
I(0) (reciprocal space) i0_reciprocal	38440000.0000
Solution quality estimate total_estimate	0.8938
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.171
Kurtosis Kurtosis kurtosis	-0.468
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8960000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.996

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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	PROTEIN FAM105B
Molecular weight formula_weight	31894.6 kDa
EC 编号 ec_number	3.4.19.12
Mutation mutation	YES
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	3754

GPLSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEEVSQKFTSIRRVRGDNYAALRATLFQAMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWKLGLKFDGKNEDLVDKIKESLTLLRKKWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAVKFLMLNRAIELYNDKEKGKEVPFFSVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMFLLAYAVRHTIQVYRLSKYNTEEFITVYPTDPPKDWPVVTLIAEDDRHYNIPVRVCEETSL

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	POLYUBIQUITIN-C
Molecular weight formula_weight	17135.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	370

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3znzb1
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

Domain ID domain_id	d3znzb2
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

CATH v4.4 (2 domains)

Domain ID domain_id	3znzB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3znzB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	100.020 Å
Unit-cell length b length_b	100.020 Å
Unit-cell length c length_c	280.260 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	42.802 Å
R factor r_factor	0.1857
R_work r_work	0.1839
R_free r_free	0.2220

fit	/app/data/saxs_computation/zn/3znz/3znz.fit
pddf	/app/data/pr_computation/zn/3znz/3znz.pr.out
profile	/app/data/saxs_computation/zn/3znz/3znz.dat

Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin

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

PROTEIN FAM105B

State in the Current Structure

Other States of the Same Protein in the Database

POLYUBIQUITIN-C

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

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)