SAXSdb — 4ilw

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

Metalloproteinase inhibitor 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 27–220	Fragment：Tissue inhibitor of metalloproteinases-2	Stromelysin-2 × 1 （P09238） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 27–220	Fragment：Tissue inhibitor of metalloproteinases-2	Stromelysin-2 × 1 （P09238） 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

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 4ILW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BR9 HUMAN TISSUE INHIBITOR OF METALLOPROTEINASE-2 Deposited 1998-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–220（194 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.10 Å R-free 0.271
1GXD proMMP-2/TIMP-2 complex Deposited 2002-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 27–220（194 aa）	Not recorded	SO4 SULFATE ION × 1 ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.50	Resolution 3.10 Å R-free 0.333
1GXD proMMP-2/TIMP-2 complex Deposited 2002-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 27–220（194 aa）	Not recorded	SO4 SULFATE ION × 1 ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.50	Resolution 3.10 Å R-free 0.333
2TMP N-TERMINAL DOMAIN OF TISSUE INHIBITOR OF METALLOPROTEINASE-2 (N-TIMP-2), NMR, 49 STRUCTURES Deposited 1998-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–153（127 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-127	Mutation：A21T	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；308 K；Ionic strength (raw mmCIF value) 125 mM；Pressure 1 NMR sample composition AQUEOUS	Resolution not provided

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

View Construct and Data Evidence

UniProt name	TIMP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–194； UniProt 27–220 Author chain B； PDBConstruct 1–194； UniProt 27–220

Stromelysin-2

Homo sapiens

UniProt P09238

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 99–263	Fragment：Matrix metalloproteinase-10 catalytic domain	Metalloproteinase inhibitor 2 × 1 （P16035） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 99–263	Fragment：Matrix metalloproteinase-10 catalytic domain	Metalloproteinase inhibitor 2 × 1 （P16035） 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

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 4ILW	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 oligomeric state 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 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
9CSX matrix metalloproteinase-10 proenzyme Deposited 2024-07-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–291（274 aa）	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

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

View Construct and Data Evidence

UniProt name	MMP10_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–165； UniProt 99–263 Author chain F； PDBConstruct 1–165； UniProt 99–263

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ilw
Deposition date deposition_date	2013-01-01
Structure title title	Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-2 (TIMP-2)
Keywords keywords	Metzincin, OB-fold, Metalloproteinase, Protease inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.27 Å
Radius of gyration Rg (electron density) rg_electron	29.72 Å
Forward intensity I(0) i0	96923300.00
Molecular weight molecular_weight	76961.0 kDa
Excluded volume excluded_volume	95763 Å³
Envelope volume envelope_volume	120870 Å³
Hydration-shell volume shell_volume	34193 Å³
Envelope diameter envelope_diameter	95.7 Å
Shell Rg shell_rg	36.62 Å
Envelope Rg envelope_rg	29.45 Å
Shape Rg shape_rg	29.71 Å
Total Rg total_rg	30.38 Å
Total atoms total_atoms	5388
Residues n_residues	682
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

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

Maximum dimension Dmax dmax	95.7 Å
Rg (real space) rg_real	30.26 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	9.6920e+07
I(0) uncertainty (real space) i0_real_error	1.5320e+06
Rg (reciprocal space) rg_reciprocal	30.27 Å
I(0) (reciprocal space) i0_reciprocal	96920000.0000
Solution quality estimate total_estimate	0.9046
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.286
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21580000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.934

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Metalloproteinase inhibitor 2
Molecular weight formula_weight	21783.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5564

CSCSPVHPQQAFCNADVVIRAKAVSEKEVDSGNDIYGNPIKRIQYEIKQIKMFKGPEKDIEFIYTAPSSAVCGVSLDVGGKKEYLIAGKAEGDGKMHITLCDFIVPWDTLSTTQKKSLNHRYQMGCECKITRCPMIPCYISSPDECLWMDWVTEKNINGHQAKFFACIKRSDGSCAWYRGAAPPKQEFLDIEDP

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Stromelysin-2
Molecular weight formula_weight	18570.6 kDa
EC 编号 ec_number	3.4.24.22
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

FSSFPGMPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDFYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYG

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

Entity 3 Entity 3 non-polymer

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

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	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	160

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ilwa_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.3 — TIMP-like
Family Family family	b.40.3.1 — Tissue inhibitor of metalloproteinases, TIMP

Domain ID domain_id	d4ilwb_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.3 — TIMP-like
Family Family family	b.40.3.1 — Tissue inhibitor of metalloproteinases, TIMP

Domain ID domain_id	d4ilwd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

Domain ID domain_id	d4ilwf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (6 domains)

Domain ID domain_id	4ilwA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	370 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1

Domain ID domain_id	4ilwA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	4ilwB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	370 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1

Domain ID domain_id	4ilwB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	4ilwD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4ilwF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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8. Citations (1)

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Unit-cell length a length_a	37.687 Å
Unit-cell length b length_b	56.934 Å
Unit-cell length c length_c	82.592 Å
Unit-cell angle α angle_alpha	76.14 °
Unit-cell angle β angle_beta	79.84 °
Unit-cell angle γ angle_gamma	71.25 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.103 Å
Low-resolution limit resolution_low	40.580 Å
R factor r_factor	0.2187
R_work r_work	0.2163
R_free r_free	0.2631

fit	/app/data/saxs_computation/il/4ilw/4ilw.fit
pddf	/app/data/pr_computation/il/4ilw/4ilw.pr.out
profile	/app/data/saxs_computation/il/4ilw/4ilw.dat

Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-2 (TIMP-2)

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

Metalloproteinase inhibitor 2

State in the Current Structure

Other States of the Same Protein in the Database

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)