SAXSdb — 7uaf

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Meprin A subunit alpha

Homo sapiens

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 × 4 其他Polymer 14 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 22–600 Chain B； UniProt 22–600 Chain C； UniProt 22–600 Chain D； UniProt 22–600	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 M6X N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide × 4 CA CALCIUM ION × 8 ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE；3 s blot, -3 force	Resolution 2.40 Å

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 7UAF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7UAB Human pro-meprin alpha (zymogen state) Deposited 2022-03-12	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 22–600（579 aa） Chain D 22–600（579 aa） Chain E 22–600（579 aa） Chain H 22–600（579 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CA CALCIUM ION × 7 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force	Resolution 3.70 Å
7UAC Human pro-meprin alpha (zymogen state) Deposited 2022-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain H 22–600（579 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force	Resolution 2.70 Å
7UAE Human meprin alpha (active state) Deposited 2022-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–600（579 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force	Resolution 2.60 Å
7UAI Meprin alpha helix in complex with fetuin-B Deposited 2022-03-13	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 22–600（579 aa） Chain C 22–600（579 aa） Chain D 22–600（579 aa） Chain E 22–600（579 aa）	Not recorded	CA CALCIUM ION × 8 ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force	Resolution 2.80 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MEP1A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–587； UniProt 22–600 Author chain B； PDBConstruct 9–587； UniProt 22–600 Author chain C； PDBConstruct 9–587； UniProt 22–600 Author chain D； PDBConstruct 9–587； UniProt 22–600

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7uaf
Deposition date deposition_date	2022-03-12
Structure title title	Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide)
Keywords keywords	Metalloprotease, complex, helical, extracellular, ONCOPROTEIN; ONCOPROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	49.31 Å
Radius of gyration Rg (electron density) rg_electron	49.47 Å
Forward intensity I(0) i0	984359000.00
Molecular weight molecular_weight	253850.0 kDa
Excluded volume excluded_volume	314440 Å³
Envelope volume envelope_volume	440740 Å³
Hydration-shell volume shell_volume	77334 Å³
Envelope diameter envelope_diameter	188.7 Å
Shell Rg shell_rg	49.90 Å
Envelope Rg envelope_rg	49.06 Å
Shape Rg shape_rg	49.49 Å
Total Rg total_rg	49.45 Å
Total atoms total_atoms	17864
Residues n_residues	2131
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	175.2 Å
Rg (real space) rg_real	49.77 Å
Rg uncertainty (real space) rg_real_error	1.83 Å
I(0) (real space) i0_real	9.8440e+08
I(0) uncertainty (real space) i0_real_error	1.8210e+07
Rg (reciprocal space) rg_reciprocal	49.31 Å
I(0) (reciprocal space) i0_reciprocal	983800000.0000
Solution quality estimate total_estimate	0.8291
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.3 Å
Skewness Skewness skewness	0.555
Kurtosis Kurtosis kurtosis	-0.215
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	110700000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.758

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Meprin A subunit alpha
Molecular weight formula_weight	67285.8 kDa
EC 编号 ec_number	3.4.24.18
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D
Atom count atom_count	17864

WSHPQFEKVPIKYLPEENVHDADFGEQKDISEINLAAGLDLFQGDILLQKSRNGLRDPNTRWTFPIPYILADNLGLNAKGAILYAFEMFRLKSCVDFKPYEGESSYIIFQQFDGCWSEVGDQHVGQNISIGQGCAYKAIIEHEILHALGFYHEQSRTDRDDYVNIWWDQILSGYQHNFDTYDDSLITDLNTPYDYESLMHYQPFSFNKNASVPTITAKIPEFNSIIGQRLDFSAIDLERLNRMYNCTTTHTLLDHCTFEKANICGMIQGTRDDTDWAHQDSAQAGEVDHTLLGQCTGAGYFMQFSTSSGSAEEAALLESRILYPKRKQQCLQFFYKMTGSPSDRLVVWVRRDDSTGNVRKLVKVQTFQGDDDHNWKIAHVVLKEEQKFRYLFQGTKGDPQNSTGGIYLDDITLTETPCPTGVWTVRNFSQVLENTSKGDKLQSPRFYNSEGYGFGVTLYPNSRESSGYLRLAFHVCSGENDAILEWPVENRQVIITILDQEPDVRNRMSSSMVFTTSKSHTSPAINDTVIWDRPSRVGTYHTDCNCFRSIDLGWSGFISHQMLKRRSFLKNDDLIIFVDFEDITHLS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Drosophila melanogaster

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	8

Entity 3 Entity 3 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	627.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide
Molecular weight formula_weight	372.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	235162

fit	/app/data/saxs_computation/ua/7uaf/7uaf.fit
pddf	/app/data/pr_computation/ua/7uaf/7uaf.pr.out
profile	/app/data/saxs_computation/ua/7uaf/7uaf.dat

Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide)