SAXSdb — 9csx

▼

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

Stromelysin-2

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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 18–291	Not recorded	IMD IMIDAZOLE × 2 ACY ACETIC ACID × 1 CA CALCIUM ION × 4 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M zinc acetate, 0.1 M imidazole, pH 7.5 and 17 % (w/v)PEG 3000, 4.0 % (v/v) acetonitrile	Resolution 1.67 Å R-free 0.213

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 9CSX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Q3A Crystal structure of the catalytic domain of human matrix metalloproteinase 10 Deposited 2003-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 99–263（165 aa） Fragment：catalytic domain Chain B 99–263（165 aa） Fragment：catalytic domain	Mutation：F170N Mutation：F170N	ZN ZINC ION × 4 CA CALCIUM ION × 6 NGH N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Tris-HCl, PEG 6000, Acetohydroxamic acid, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.298
1Q3A Crystal structure of the catalytic domain of human matrix metalloproteinase 10 Deposited 2003-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 99–263（165 aa） Fragment：catalytic domain Chain C 99–263（165 aa） Fragment：catalytic domain	Mutation：F170N Mutation：F170N	ZN ZINC ION × 4 CA CALCIUM ION × 6 NGH N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Tris-HCl, PEG 6000, Acetohydroxamic acid, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.298
1Q3A Crystal structure of the catalytic domain of human matrix metalloproteinase 10 Deposited 2003-07-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 99–263（165 aa） Fragment：catalytic domain	Mutation：F170N	ZN ZINC ION × 2 CA CALCIUM ION × 3 NGH N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Tris-HCl, PEG 6000, Acetohydroxamic acid, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.298
3V96 Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-1 (TIMP-1) Deposited 2011-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 99–263（165 aa） Fragment：unp residues 99-263	Not recorded	PO4 PHOSPHATE ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；298 K；0.1 M sodium dihydrogen phosphate solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.266
4ILW Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-2 (TIMP-2) Deposited 2013-01-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 99–263（165 aa） Fragment：Matrix metalloproteinase-10 catalytic domain	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.1 M HEPES pH 7.5, 25 % (w/v) PEG 2000 MME, VAPOR DIFFUSION, temperature 298K	Resolution 2.10 Å R-free 0.263
4ILW Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-2 (TIMP-2) Deposited 2013-01-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 99–263（165 aa） Fragment：Matrix metalloproteinase-10 catalytic domain	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.1 M HEPES pH 7.5, 25 % (w/v) PEG 2000 MME, VAPOR DIFFUSION, temperature 298K	Resolution 2.10 Å R-free 0.263

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

View Construct and Data Evidence

UniProt name	MMP10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–274； UniProt 18–291

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	9csx
Deposition date deposition_date	2024-07-24
最后修订 last_revision	2025-08-13
Structure title title	matrix metalloproteinase-10 proenzyme
Keywords keywords	proteinase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	18.90 Å
Radius of gyration Rg (electron density) rg_electron	17.91 Å
Forward intensity I(0) i0	12794600.00
Molecular weight molecular_weight	26547.0 kDa
Excluded volume excluded_volume	33036 Å³
Envelope volume envelope_volume	38472 Å³
Hydration-shell volume shell_volume	18019 Å³
Envelope diameter envelope_diameter	65.9 Å
Shell Rg shell_rg	24.15 Å
Envelope Rg envelope_rg	18.36 Å
Shape Rg shape_rg	17.86 Å
Total Rg total_rg	19.01 Å
Total atoms total_atoms	3620
Residues n_residues	229
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	64.2 Å
Rg (real space) rg_real	18.84 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.2790e+07
I(0) uncertainty (real space) i0_real_error	1.5620e+05
Rg (reciprocal space) rg_reciprocal	18.85 Å
I(0) (reciprocal space) i0_reciprocal	12790000.0000
Solution quality estimate total_estimate	0.6905
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.197
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	3003000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.996; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Stromelysin-2
Molecular weight formula_weight	30718.5 kDa
EC 编号 ec_number	3.4.24.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3881

YPLSGAAKEEDSNKDLAQQYLEKYYNLEKDVKQFRRKDSNLIVKKIQGMQKFLGLEVTGKLDTDTLEVMRKPRCGVPDVGHFSSFPGMPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDFYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYGPPPASTEEPLVPTKSVPSGSEMPAKCDP

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	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

▶

8. Citations (1)

▶

Unit-cell length a length_a	80.841 Å
Unit-cell length b length_b	72.003 Å
Unit-cell length c length_c	54.495 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	130.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	27.120 Å
R factor r_factor	0.1900
R_work r_work	0.1888
R_free r_free	0.2126

fit	/app/data/saxs_computation/cs/9csx/9csx.fit
pddf	/app/data/pr_computation/cs/9csx/9csx.pr.out
profile	/app/data/saxs_computation/cs/9csx/9csx.dat

matrix metalloproteinase-10 proenzyme

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

Stromelysin-2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction