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4gwn

Crystal structure of human mature meprin beta

Method: X-RAY DIFFRACTION Dmax: 87.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Meprin A subunit beta

Homo sapiens

UniProt Q16820

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 10 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 62–614 Fragment：Mature meprin beta ectomoiety, UNP residues 62-614 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CD CADMIUM ION × 2 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20%(wt/vol) PEG 3350, 0.2M sodium malonate, 0.1M bis-Tris propane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.00 Å R-free 0.238

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 4GWN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GWM Crystal structure of human promeprin beta Deposited 2012-09-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–614（592 aa） Fragment：Promeprin beta ectomoiety, UNP residues 23-614
Chain B 23–614（592 aa） Fragment：Promeprin beta ectomoiety, UNP residues 23-614
Mutation：T23P, P24W Mutation：T23P, P24W ZN ZINC ION × 2 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 5 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；18.2%(wt/vol) PEG8000, 1M LiCl, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.188
7AQ1 Crystal structure of human mature meprin beta in complex with the specific inhibitor MWT-S-270 Deposited 2020-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimer
Chain A 62–595（534 aa）
Chain B 62–595（534 aa）
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 RUE 3-[[(3-Carboxyphenyl)methyl-[2-(hydroxyamino)-2-oxoethyl]amino]methyl]benzoic acid × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；286 K；Protein was mixed with inhibitor in a molar ratio of 1 to 1.2 to a final protein concentration of 8 mg/mL in 30 mM Tris, 100 mM sodium chloride, pH 7.6. 200 nL protein/inhibitor was mixed with 200 nL praezipitation buffer and equilibrated against 55 micro Liter of praezipitation buffer, containing 25 percent (w/v) PEG 4000 and 30 percent (v/v) ethylene glycol.
Resolution 2.41 Å R-free 0.236
7AUW Inhibitory complex of human meprin beta with mouse fetuin-B. Deposited 2020-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 62–608（547 aa）
Chain C 62–608（547 aa）
Not recorded NA SODIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；293 K；20.0% PEG smear medium, 0.1M ammonium sulfate, 0.05M magnesium sulfate heptahydrate, 0.1M bicine pH 9.3, 10% ethylene glycol.
Resolution 2.80 Å R-free 0.261

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MEP1B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–553； UniProt 62–614

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 4gwn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gwn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gwn
Deposition date deposition_date2012-09-03
Structure title titleCrystal structure of human mature meprin beta
Keywords keywordsMultidomain structure, 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_guinier26.61 Å
Radius of gyration Rg (electron density) rg_electron25.35 Å
Forward intensity I(0) i075542800.00
Molecular weight molecular_weight65481.0 kDa
Excluded volume excluded_volume80856 ų
Envelope volume envelope_volume100420 ų
Hydration-shell volume shell_volume32412 ų
Envelope diameter envelope_diameter90.9 Å
Shell Rg shell_rg33.14 Å
Envelope Rg envelope_rg25.45 Å
Shape Rg shape_rg25.34 Å
Total Rg total_rg26.21 Å
Total atoms total_atoms4598
Residues n_residues533
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 dmax87.1 Å
Rg (real space) rg_real26.46 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real7.5540e+07
I(0) uncertainty (real space) i0_real_error1.0900e+06
Rg (reciprocal space) rg_reciprocal26.51 Å
I(0) (reciprocal space) i0_reciprocal75550000.0000
Solution quality estimate total_estimate0.8924
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.9 Å
Skewness Skewness skewness0.147
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14170000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.987
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4gwnA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id4gwnA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id4gwnA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
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8. Citations (1)

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9. Files and Curves (10)