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7v5l

Crystal structure of human bleomycin hydrolase

Method: X-RAY DIFFRACTION Dmax: 166.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bleomycin hydrolase

Homo sapiens

UniProt Q13867

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–455 Chain B； UniProt 1–455 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2M sodium chloride, 10% (w/v) PEG 8000, 0.1mM CHES, pH 9.5 Resolution 1.74 Å R-free 0.200
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain C； UniProt 1–455 Chain D； UniProt 1–455 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2M sodium chloride, 10% (w/v) PEG 8000, 0.1mM CHES, pH 9.5 Resolution 1.74 Å R-free 0.200

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 7V5L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CB5 HUMAN BLEOMYCIN HYDROLASE. Deposited 1999-03-01 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 2–454（453 aa）
Chain B 2–454（453 aa）
Chain C 2–454（453 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 2.59 Å R-free 0.260
2CB5 HUMAN BLEOMYCIN HYDROLASE, C73S/DELE455 MUTANT Deposited 1999-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–454（453 aa）
Chain B 2–454（453 aa）
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 1.85 Å R-free 0.210
2CB5 HUMAN BLEOMYCIN HYDROLASE, C73S/DELE455 MUTANT Deposited 1999-03-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 2–454（453 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 1.85 Å R-free 0.210
2CB5 HUMAN BLEOMYCIN HYDROLASE, C73S/DELE455 MUTANT Deposited 1999-03-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain B 2–454（453 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 1.85 Å R-free 0.210
7V5S Crystal structure of human bleomycin hydrolase C73A mutant Deposited 2021-08-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–455（455 aa）
Mutation：C73A PG4 TETRAETHYLENE GLYCOL × 6 PGE TRIETHYLENE GLYCOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% (w/v) PEG 400, 0.1mM CHES, pH 9.5
Resolution 3.02 Å R-free 0.197
7V5T Crystal structure of human bleomycin hydrolase C73S mutant Deposited 2021-08-18 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–455（455 aa）
Mutation：C73S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% (w/v) PEG 400, 0.1mM CHES, pH 9.5
Resolution 3.25 Å R-free 0.193
7XF9 Crystal structure of human bleomycin hydrolase H372A mutant Deposited 2022-04-01 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–455（455 aa）
Mutation：H372A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；30% (w/v) PEG 400, 0.1mM CHES
Resolution 3.20 Å R-free 0.242

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

View Construct and Data Evidence
UniProt name BLMH_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–475； UniProt 1–455 Author chain B； PDBConstruct 21–475； UniProt 1–455 Author chain C； PDBConstruct 21–475； UniProt 1–455 Author chain D； PDBConstruct 21–475； UniProt 1–455

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 7v5l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7v5l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7v5l
Deposition date deposition_date2021-08-17
Structure title titleCrystal structure of human bleomycin hydrolase
Keywords keywordscysteine protease, 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_guinier52.41 Å
Radius of gyration Rg (electron density) rg_electron53.10 Å
Forward intensity I(0) i0624619000.00
Molecular weight molecular_weight208760.0 kDa
Excluded volume excluded_volume261410 ų
Envelope volume envelope_volume354660 ų
Hydration-shell volume shell_volume59212 ų
Envelope diameter envelope_diameter176.0 Å
Shell Rg shell_rg49.87 Å
Envelope Rg envelope_rg52.73 Å
Shape Rg shape_rg53.10 Å
Total Rg total_rg52.98 Å
Total atoms total_atoms14676
Residues n_residues1808
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 dmax166.6 Å
Rg (real space) rg_real52.95 Å
Rg uncertainty (real space) rg_real_error1.71 Å
I(0) (real space) i0_real6.2460e+08
I(0) uncertainty (real space) i0_real_error1.0910e+07
Rg (reciprocal space) rg_reciprocal51.92 Å
I(0) (reciprocal space) i0_reciprocal623700000.0000
Solution quality estimate total_estimate0.5027
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9 Å
Skewness Skewness skewness0.522
Kurtosis Kurtosis kurtosis-0.672
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha69370000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.575; Stabil: 0.999; Sysdev: 0.007; Positv: 1.000; Valcen: 0.775; Smooth: 0.012
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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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8. Citations (1)

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9. Files and Curves (10)