SAXSdb — 8p1p

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

Ubiquitin carboxyl-terminal hydrolase 28

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 149–458 Chain A； UniProt 529–707 Chain B； UniProt 149–458 Chain B； UniProt 529–707	Not recorded	CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1 WF0 2-[[5-bromanyl-2-[[4-fluoranyl-3-(trifluoromethyl)phenyl]methoxy]phenyl]methylamino]ethanol × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.5 M sodium malonate pH 6.0 0.1 M sodium citrate pH 5.0	Resolution 2.76 Å R-free 0.241

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 8P1P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LVA NMR solution structure of the N-terminal domain of human USP28, Northeast structural genomics consortium target HT8470A Deposited 2012-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–132（111 aa） Fragment：UIM domain residues 22-132	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 450；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N] protein, 10 mM mops, 450 mM sodium chloride, 10 uM ZnSO4, 1 mM DTT, 0.01 % NaN3, 1 mM benzamidine, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MUU The Proteolytic Activity of Ubiquitin-specific Protease 28 Is Modulated by the N-terminal Domain Deposited 2014-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal Domain (UNP residues 1-120)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298.2 K；Ionic strength (raw mmCIF value) 0.15；Pressure 1 NMR sample composition 10 % D20, 90 % H20, 0.8-1.0 mM [U-15N] USP, 20 mM Na2HPO4/NaH2PO4, 100 mM NaCl, 2 mM DTT, 0.02 % NaNH3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 % D20, 90 % H20, 0.8-1.0 mM [U-15N; U-13C] USP, 20 mM Na2HPO4/NaH2PO4, 100 mM NaCl, 2 mM DTT, 0.02 % NaNH3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 100 % D20, 0.8-1.0 mM [U-15N; U-13C] USP, 20 mM Na2HPO4/NaH2PO4, 100 mM NaCl, 2 mM DTT, 0.02 % NaNH3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6H4H Usp28 catalytic domain variant E593D in complex with UbPA Deposited 2018-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 149–707（559 aa） Chain B 149–707（559 aa）	Mutation：E593D Mutation：E593D	SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M Citrate pH 5.0 0.8 M Ammonium Sulfate	Resolution 3.50 Å R-free 0.280
6H4I Usp28 catalytic domain apo Deposited 2018-07-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–707（560 aa） Chain C 148–707（560 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M citric acid pH 5.0 0.8 M Ammonium Sulfate	Resolution 3.22 Å R-free 0.196
6HEH Structure of the catalytic domain of USP28 (insertion deleted) Deposited 2018-08-20	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 149–399（251 aa） Chain A 580–703（124 aa）	Mutation：;residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS ; Mutation：;residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS ;	EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；291 K；12% (w/v) PEG 8000, 100 mM sodium chloride, 200 mM lithium sulfate, 100 mM MES pH 6.6	Resolution 2.26 Å R-free 0.216
6HEI Structure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA Deposited 2018-08-20	Different construct Different mutation/modification 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 149–399（251 aa） Chain A 580–703（124 aa）	Mutation：;residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS ; Mutation：;residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS ;	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；22% (w/v) PEG 3350, 300 mM potassium sodium tartrate	Resolution 1.64 Å R-free 0.214
6HEJ Structure of human USP28 Deposited 2018-08-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 149–703（555 aa） Chain B 149–703（555 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.8 M ammonium sulfate, 100 mM sodium citrate pH 5.5	Resolution 2.79 Å R-free 0.286
6HEK Structure of human USP28 bound to Ubiquitin-PA Deposited 2018-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 149–703（555 aa） Chain C 149–703（555 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；8% (w/v) PEG 3350, 200 mM ammonium acetate and 100 mM sodium citrate pH 5.4	Resolution 3.03 Å R-free 0.237
7TUO Crystal structure analysis of human USP28 complex with a compound Deposited 2022-02-03	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 149–399（251 aa） Chain A 580–703（124 aa）	Not recorded	KL9 7-amino-N-(2-{4-[(1R,3s,5S)-8-azabicyclo[3.2.1]octan-3-yl]phenyl}ethyl)-3-methylthieno[2,3-b]pyrazine-6-carboxamide × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.4M Sodium maleic acid, pH 8.0	Resolution 1.96 Å R-free 0.203
8HJE Vismodegib binds to the catalytical domain of human Ubiquitin-Specific Protease 28 Deposited 2022-11-23	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 150–399（250 aa） Chain A 580–703（124 aa）	Not recorded	VIS 2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；0.1 M Bis-tris propane pH 6.4, 0.2 M potassium thiocyanate, 20% PEG3350 and 3% sucrose	Resolution 2.85 Å R-free 0.254
8P14 USP28 USP domain in complex with Vismodegib Deposited 2023-05-11	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 149–399（251 aa） Chain A 580–698（119 aa）	Not recorded	VIS 2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide × 1 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M NaCl 0.1 M Li2SO4 0.1 M MES pH 6.4 14% PEG4000	Resolution 2.57 Å R-free 0.218
8P19 USP28 USP domain apo Deposited 2023-05-11	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 149–399（251 aa） Chain A 580–698（119 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05M NaCl 0.1M Li2SO4 0.1M MES pH 6.4 14% PEG4000	Resolution 2.45 Å R-free 0.222
8P1Q USP28 in complex with FT206 Deposited 2023-05-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 149–458（310 aa） Chain A 529–707（179 aa） Chain B 149–458（310 aa） Chain B 529–707（179 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 WFT 3-azanyl-N-[(2S)-6-[(1S,5R)-3,8-diazabicyclo[3.2.1]octan-3-yl]-1,2,3,4-tetrahydronaphthalen-2-yl]-6-methyl-thieno[2,3-b]pyridine-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.5 M Na-malonate, pH6.0 0.1M Na-citrate, pH 5.0	Resolution 2.79 Å R-free 0.235
9SUU USP28 USP domain in complex with T-10531 Deposited 2025-09-30	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 149–399（251 aa） Chain A 580–698（119 aa）	Not recorded	CL CHLORIDE ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1JQP ~{N}-[3-[[4-bromanyl-5-fluoranyl-2-[[(3~{S})-3-oxidanylpyrrolidin-1-yl]methyl]phenoxy]methyl]-2,4,5-tris(fluoranyl)phenyl]-2-chloranyl-4-methylsulfonyl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.05 M sodium chloride, 0.2 M lithium sulfate, 0.1 M MES pH 6.4, 14 % PEG6000	Resolution 2.75 Å R-free 0.245

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

View Construct and Data Evidence

UniProt name	UBP28_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–311； UniProt 149–458 Author chain A； PDBConstruct 316–494； UniProt 529–707 Author chain B； PDBConstruct 2–311； UniProt 149–458 Author chain B； PDBConstruct 316–494； UniProt 529–707

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	8p1p
Deposition date deposition_date	2023-05-12
Structure title title	USP28 in complex with AZ1
Keywords keywords	USP28, Ubiquitin, inhibitor, AZ1, ONCOPROTEIN; ONCOPROTEIN
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	35.21 Å
Radius of gyration Rg (electron density) rg_electron	34.50 Å
Forward intensity I(0) i0	160491000.00
Molecular weight molecular_weight	101230.0 kDa
Excluded volume excluded_volume	126420 Å³
Envelope volume envelope_volume	178350 Å³
Hydration-shell volume shell_volume	43475 Å³
Envelope diameter envelope_diameter	119.4 Å
Shell Rg shell_rg	40.26 Å
Envelope Rg envelope_rg	34.54 Å
Shape Rg shape_rg	34.50 Å
Total Rg total_rg	34.97 Å
Total atoms total_atoms	7129
Residues n_residues	869
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	111.1 Å
Rg (real space) rg_real	35.14 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	1.6050e+08
I(0) uncertainty (real space) i0_real_error	2.6030e+06
Rg (reciprocal space) rg_reciprocal	35.18 Å
I(0) (reciprocal space) i0_reciprocal	160500000.0000
Solution quality estimate total_estimate	0.8964
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.221
Kurtosis Kurtosis kurtosis	-0.501
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16730000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.778

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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	Ubiquitin carboxyl-terminal hydrolase 28
Molecular weight formula_weight	57924.2 kDa
EC 编号 ec_number	3.4.19.12
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	7206

GPNPNDWRRVDGWPVGLKNVGNTCWFSAVIQSLFQLPEFRRLVLSYSLPQNVLENCRSHTEKRNIMFMQELQYLFALMMGSNRKFVDPSAALDLLKGAFRSSEEQQQDVSEFTHKLLDWLEDAFQLAVNVNSHRNKSENPMVQLFYGTFLTEGVREGKPFCNNETFGQYPLQVNGYRNLDECLEGAMVEGDVELLPSDHSVKYGQERWFTKLPPVLTFELSRFEFNQSLGQPEKIHNKLEFPQIIYMDRYMYRSKELIRNKRECIRKLKEEIKILQQKLERYVKYGSGPARFPLPDMLKYVIEFASTKPASSGSGAPRTVTDEEINFVKTCLQRWRSEIEQDIQDLKTCIASTTQTIEQMYCDPLLRQVPYRLHAVLVHEGQANAGHYWAYIYNQPRQSWLKYNDISVTESSWEEVERDSYGGLRNVSAYCLMYINDKLPYFNAEAAPTESDQMSEVEALSVELKHYIQEDNWRFEQEVEEWEEEQSCKIPQME

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 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-[[5-bromanyl-2-[[4-fluoranyl-3-(trifluoromethyl)phenyl]methoxy]phenyl]methylamino]ethanol
Molecular weight formula_weight	422.2 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	47

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8. Citations (2)

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Unit-cell length a length_a	100.444 Å
Unit-cell length b length_b	105.541 Å
Unit-cell length c length_c	178.708 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	8

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.760 Å
Low-resolution limit resolution_low	48.350 Å
R factor r_factor	0.2138
R_work r_work	0.2128
R_free r_free	0.2410

fit	/app/data/saxs_computation/p1/8p1p/8p1p.fit
pddf	/app/data/pr_computation/p1/8p1p/8p1p.pr.out
profile	/app/data/saxs_computation/p1/8p1p/8p1p.dat

USP28 in complex with AZ1

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

Ubiquitin carboxyl-terminal hydrolase 28

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