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2hd5

USP2 in complex with ubiquitin

Method: X-RAY DIFFRACTION Dmax: 72.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 2

Homo sapiens

UniProt O75604

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 258–605 Fragment：residues 258-605 Polyubiquitin × 1 （Q24K23） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：LIQUID DIFFUSION；pH 6.5；295 K；200 mM MgCl2, 25% PEG 3550, 100 mM Bis-Tris, Protein at 11.8 mg/ml, pH 6.5, LIQUID DIFFUSION, temperature 295K Resolution 1.85 Å R-free 0.229

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 2HD5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2IBI Covalent Ubiquitin-USP2 Complex Deposited 2006-09-11 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 250–605（356 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 251-605
Mutation：E472A, K473A ZN ZINC ION × 1 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；298 K；22% PEG1500, 0.1 M Bicine, 0.2 M NaCl, 1 mM DTT, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 9.00
Resolution 2.20 Å R-free 0.259
3NHE High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin Deposited 2010-06-14 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 258–605（348 aa） Fragment：UNP residues 258-605
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；5% PEG4000, 0.1M Hepes, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.26 Å R-free 0.189
3V6C Crystal Structure of USP2 in complex with mutated ubiquitin Deposited 2011-12-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 258–605（348 aa）
Not recorded CL CHLORIDE ION × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；21% PEG 3350,0.2 M CaCl, 0.1 Bis-Tris pH 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.220
3V6E Crystal Structure of USP2 and a mutant form of Ubiquitin Deposited 2011-12-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 258–605（348 aa）
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；21% PEG3350, 0.2 M Calcium Chloride,0.1 Bis-Tris pH 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.234
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 A 258–605（348 aa） Fragment：UNP residues 258-605
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 mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 258–605（348 aa） Fragment：UNP residues 258-605
Mutation：C276S 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
6DGF Ubiquitin Variant bound to USP2 Deposited 2018-05-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 250–605（356 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES buffer pH 6, 12% (w/v) PEG3350, 0.2M sodium sulfate
Resolution 2.34 Å R-free 0.224

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBP2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–348； UniProt 258–605

Polyubiquitin

OrganismNot specified

UniProt Q24K23

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 1–76 Fragment：residues 1-76 Ubiquitin carboxyl-terminal hydrolase 2 × 1 （O75604） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：LIQUID DIFFUSION；pH 6.5；295 K；200 mM MgCl2, 25% PEG 3550, 100 mM Bis-Tris, Protein at 11.8 mg/ml, pH 6.5, LIQUID DIFFUSION, temperature 295K Resolution 1.85 Å R-free 0.229

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 Q24K23_BOVIN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 2hd5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hd5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hd5
Deposition date deposition_date2006-06-20
Structure title titleUSP2 in complex with ubiquitin
Keywords keywordsdeubiquitinating protease, cysteine protease, substrate enzyme complex, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.02 Å
Radius of gyration Rg (electron density) rg_electron20.50 Å
Forward intensity I(0) i034579200.00
Molecular weight molecular_weight44581.0 kDa
Excluded volume excluded_volume55420 ų
Envelope volume envelope_volume62790 ų
Hydration-shell volume shell_volume24965 ų
Envelope diameter envelope_diameter72.1 Å
Shell Rg shell_rg27.89 Å
Envelope Rg envelope_rg20.70 Å
Shape Rg shape_rg20.43 Å
Total Rg total_rg21.59 Å
Total atoms total_atoms3127
Residues n_residues363
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax72.4 Å
Rg (real space) rg_real21.89 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real3.4580e+07
I(0) uncertainty (real space) i0_real_error4.5620e+05
Rg (reciprocal space) rg_reciprocal21.91 Å
I(0) (reciprocal space) i0_reciprocal34580000.0000
Solution quality estimate total_estimate0.8802
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.1 Å
Skewness Skewness skewness0.219
Kurtosis Kurtosis kurtosis-0.285
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha6840000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2hd5a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.9 — Ubiquitin carboxyl-terminal hydrolase, UCH
Domain ID domain_idd2hd5b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (2 domains)

Domain ID domain_id2hd5A00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id2hd5B00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)