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2cb5

HUMAN BLEOMYCIN HYDROLASE, C73S/DELE455 MUTANT

Method: X-RAY DIFFRACTION Dmax: 130.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–454 Chain B； UniProt 2–454 Mutation：YES No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.00 Resolution 1.85 Å R-free 0.210
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 2–454 Mutation：YES No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.00 Resolution 1.85 Å R-free 0.210
3 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 2–454 Mutation：YES No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.00 Resolution 1.85 Å R-free 0.210

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 2CB5 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 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
7V5L Crystal structure of human bleomycin hydrolase Deposited 2021-08-17 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）
Chain B 1–455（455 aa）
Not recorded No recorded non-water small molecule 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
7V5L Crystal structure of human bleomycin hydrolase Deposited 2021-08-17 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain C 1–455（455 aa）
Chain D 1–455（455 aa）
Not recorded No recorded non-water small molecule 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
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 6 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 1–453； UniProt 2–454 Author chain B； PDBConstruct 1–453； UniProt 2–454

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 2cb5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2cb5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2cb5
Deposition date deposition_date1999-03-02
Structure title titleHUMAN BLEOMYCIN HYDROLASE, C73S/DELE455 MUTANT
Keywords keywordsHYDROLASE, AMINOPEPTIDASE, CYSTEINE PROTEASE, SELF-COMPARTMENTALIZING, BLEOMYCIN, CYLINASE; 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_guinier38.39 Å
Radius of gyration Rg (electron density) rg_electron38.40 Å
Forward intensity I(0) i0166502000.00
Molecular weight molecular_weight104500.0 kDa
Excluded volume excluded_volume130770 ų
Envelope volume envelope_volume180910 ų
Hydration-shell volume shell_volume40663 ų
Envelope diameter envelope_diameter132.7 Å
Shell Rg shell_rg42.16 Å
Envelope Rg envelope_rg38.45 Å
Shape Rg shape_rg38.40 Å
Total Rg total_rg38.62 Å
Total atoms total_atoms7348
Residues n_residues906
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 dmax130.5 Å
Rg (real space) rg_real38.73 Å
Rg uncertainty (real space) rg_real_error1.32 Å
I(0) (real space) i0_real1.6650e+08
I(0) uncertainty (real space) i0_real_error3.1600e+06
Rg (reciprocal space) rg_reciprocal38.53 Å
I(0) (reciprocal space) i0_reciprocal166500000.0000
Solution quality estimate total_estimate0.8315
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.8 Å
Skewness Skewness skewness0.459
Kurtosis Kurtosis kurtosis-0.470
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21500000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.812; Smooth: 0.567
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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_idd2cb5a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.1 — Papain-like
Domain ID domain_idd2cb5b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.1 — Papain-like

CATH v4.4 (2 domains)

Domain ID domain_id2cb5A01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id2cb5B01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
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8. Citations (1)

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9. Files and Curves (10)