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2hl9

SUMO protease Ulp1 with the catalytic cysteine oxidized to a sulfonic acid

Method: X-RAY DIFFRACTION Dmax: 60.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-like-specific protease 1

Saccharomyces cerevisiae

UniProt Q02724

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 403–621 Fragment：c-terminal catalytic domain Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；30%(v/v) pentaerythritol ethoxylate(15/4 EO/OH), 0.05M ammonium sulfate, 100mM hydrogen peroxide , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 1.90 Å R-free 0.237

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 2HL9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EUV X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX WITH SMT3, THE YEAST ORTHOLOG OF SUMO. Deposited 2000-04-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–621（221 aa） Fragment：C-TERMINAL PROTEASE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M MES pH6.5, 10% w/v polyethylene glycol 20000, 3% w/v 1,6-hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.60 Å R-free 0.251
2HKP SUMO protease Ulp1 with the catalytic cysteine oxidized to a sulfenic acid Deposited 2006-07-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 403–621（219 aa） Fragment：c-terminal catalytic domain
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；20% w/v PEG 3350, 0.2M NaCl and post-soaked in 50mM DTT for 48 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.10 Å R-free 0.260
2HL8 SUMO protease Ulp1 with the catalytic cysteine oxidized to a sulfinic acid Deposited 2006-07-06 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 403–621（219 aa） Fragment：c-terminal catalytic domain
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；20%(w/v) PEG 3350, 0.2M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.234
5H2V Crystal structure of the karyopherin Kap121p bound to the SUMO protease Ulp1p Deposited 2016-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–150（150 aa） Fragment：UNP residues 1-150
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG20000
Resolution 2.80 Å R-free 0.241
5H2W Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340) Deposited 2016-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 150–340（191 aa） Fragment：UNP residues 150-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M MES, 0.1M calcium acetate, 12% PEG8000
Resolution 2.50 Å R-free 0.247
5H2W Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340) Deposited 2016-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 150–340（191 aa） Fragment：UNP residues 150-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M MES, 0.1M calcium acetate, 12% PEG8000
Resolution 2.50 Å R-free 0.247
5H2X Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-172) Deposited 2016-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 150–172（23 aa） Fragment：UNP residues 150-172
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium phosphate, 12% PEG8000
Resolution 2.20 Å R-free 0.228

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

View Construct and Data Evidence
UniProt name ULP1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–221； UniProt 403–621

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 2hl9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hl9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hl9
Deposition date deposition_date2006-07-06
Structure title titleSUMO protease Ulp1 with the catalytic cysteine oxidized to a sulfonic acid
Keywords keywordshydrolase; 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_guinier18.60 Å
Radius of gyration Rg (electron density) rg_electron17.32 Å
Forward intensity I(0) i011269800.00
Molecular weight molecular_weight25173.0 kDa
Excluded volume excluded_volume31596 ų
Envelope volume envelope_volume35743 ų
Hydration-shell volume shell_volume17282 ų
Envelope diameter envelope_diameter61.7 Å
Shell Rg shell_rg23.51 Å
Envelope Rg envelope_rg17.70 Å
Shape Rg shape_rg17.30 Å
Total Rg total_rg18.33 Å
Total atoms total_atoms1771
Residues n_residues217
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 dmax60.3 Å
Rg (real space) rg_real18.53 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real1.1270e+07
I(0) uncertainty (real space) i0_real_error1.5190e+05
Rg (reciprocal space) rg_reciprocal18.54 Å
I(0) (reciprocal space) i0_reciprocal11270000.0000
Solution quality estimate total_estimate0.8041
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.1 Å
Skewness Skewness skewness0.263
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2518000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.817; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2hl9a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.7 — Adenain-like
Domain ID domain_idd2hl9a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2hl9A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2hl9A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily130 — Ubiquitin-related
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8. Citations (2)

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9. Files and Curves (10)