SAXSdb — 1qib

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

72 kDa type IV collagenase

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 115–213 Chain A； UniProt 394–449	Fragment：CATALYTIC DOMAIN RESIDUES 88-250 WITH THE FIBRONECTIN DOMAIN DELETED	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.80 Å R-free 0.244

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 1QIB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CK7 GELATINASE A (FULL-LENGTH) Deposited 1999-04-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–660（631 aa） Fragment：FULL-LENGTH	Mutation：E404A	ZN ZINC ION × 2 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.8	Resolution 2.80 Å R-free 0.327
1CXW THE SECOND TYPE II MODULE FROM HUMAN MATRIX METALLOPROTEINASE 2 Deposited 1999-08-31	Different construct Different mutation/modification 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 278–336（59 aa） Fragment：THE SECOND TYPE II MODULE	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR measurement conditions pH 5.1；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition 1.3MM COL-2 NA; 90% H2O, 10% D2O NMR sample composition 1.3MM COL-2 NA; D2O NMR sample composition 1MM COL-2 U-15N; 90% H2O, 10% D2O NMR sample composition 4MM COL-2 U-15N; 90% H2O, 10% D2O	Resolution not provided
1EAK Catalytic domain of proMMP-2 E404Q mutant Deposited 2001-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 32–452（421 aa） Fragment：CATALYTIC DOMAIN RESIDUES 32-452 Chain C 32–452（421 aa） Fragment：CATALYTIC DOMAIN RESIDUES 32-452	Mutation：YES Mutation：YES	SO4 SULFATE ION × 3 ZN ZINC ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PH 8.50	Resolution 2.66 Å R-free 0.303
1EAK Catalytic domain of proMMP-2 E404Q mutant Deposited 2001-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 32–452（421 aa） Fragment：CATALYTIC DOMAIN RESIDUES 32-452 Chain D 32–452（421 aa） Fragment：CATALYTIC DOMAIN RESIDUES 32-452	Mutation：YES Mutation：YES	SO4 SULFATE ION × 3 ZN ZINC ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PH 8.50	Resolution 2.66 Å R-free 0.303
1GEN C-TERMINAL DOMAIN OF GELATINASE A Deposited 1995-07-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 443–660（218 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.260
1GXD proMMP-2/TIMP-2 complex Deposited 2002-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 30–660（631 aa）	Mutation：YES	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–660（631 aa）	Mutation：YES	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
1HOV SOLUTION STRUCTURE OF A CATALYTIC DOMAIN OF MMP-2 COMPLEXED WITH SC-74020 Deposited 2000-12-11	Different construct Different mutation/modification 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 110–256（147 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 2 I52 N-{4-[(1-HYDROXYCARBAMOYL-2-METHYL-PROPYL)-(2-MORPHOLIN-4-YL-ETHYL)-SULFAMOYL]-4-PENTYL-BENZAMIDE × 1	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.3-0.4mM U-15N, 13C MMP-2C: unlabeled SC-74020 in 20mM TRIS-d11-HCl, 5mM CaCl2, 10uM ZnCl2, 20uM unlabeled SC-74020 \| 90% H2O/10% D2O	Resolution not provided
1J7M The Third Fibronectin Type II Module from Human Matrix Metalloproteinase 2 Deposited 2001-05-17	Different construct Different mutation/modification 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 337–394（58 aa） Fragment：third fibronectin type II module	Mutation：E11G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.4；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5mM col-3 NA; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM col-3 NA; D2O \| D2O NMR sample composition 1mM col-3 U-15n; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1KS0 The First Fibronectin Type II Module from Human Matrix Metalloproteinase 2 Deposited 2002-01-10	Different construct Different mutation/modification 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 223–282（60 aa） Fragment：First Fibronectin Type II Module	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5mM col-1; 90% H2O, 10% d6-acetone \| 90% H2O, 10% d6-acetone NMR sample composition 0.5mM col-1; 90% D2O, 10% d6-acetone \| 90% D2O, 10% d6-acetone NMR sample composition 0.7mM col-1 15N; 90% H2O, 10% d6-acetone \| 90% H2O, 10% d6-acetone	Resolution not provided
1RTG C-TERMINAL DOMAIN (HAEMOPEXIN-LIKE DOMAIN) OF HUMAN MATRIX METALLOPROTEINASE-2 Deposited 1995-12-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 451–660（210 aa） Fragment：C-TERMINAL RESIDUES 451 - 660, HAEMOPEXIN-LIKE DOMAIN	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
3AYU Crystal structure of MMP-2 active site mutant in complex with APP-drived decapeptide inhibitor Deposited 2011-05-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–219（110 aa） Fragment：UNP residues 110-219 and 394-450 Chain A 394–450（57 aa） Fragment：UNP residues 110-219 and 394-450	Mutation：E108K, Q110V, E121A Mutation：E108K, Q110V, E121A	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.205

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MMP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 115–213 Author chain A； PDBConstruct 106–161； UniProt 394–449

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	1qib
Deposition date deposition_date	1999-06-11
Structure title title	CRYSTAL STRUCTURE OF GELATINASE A CATALYTIC DOMAIN
Keywords keywords	INHIBITOR, MATRIXIN, MATRIX METALLOPROTEINASE-2 (MMP-2), GELATINASE A, METZINCIN, HYDROLASE; HYDROLASE
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	16.42 Å
Radius of gyration Rg (electron density) rg_electron	15.16 Å
Forward intensity I(0) i0	6517050.00
Molecular weight molecular_weight	18177.0 kDa
Excluded volume excluded_volume	22494 Å³
Envelope volume envelope_volume	26388 Å³
Hydration-shell volume shell_volume	14531 Å³
Envelope diameter envelope_diameter	49.2 Å
Shell Rg shell_rg	21.18 Å
Envelope Rg envelope_rg	15.43 Å
Shape Rg shape_rg	15.13 Å
Total Rg total_rg	16.34 Å
Total atoms total_atoms	1277
Residues n_residues	160
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	50.4 Å
Rg (real space) rg_real	16.28 Å
Rg uncertainty (real space) rg_real_error	0.19 Å
I(0) (real space) i0_real	6.5170e+06
I(0) uncertainty (real space) i0_real_error	7.0360e+04
Rg (reciprocal space) rg_reciprocal	16.30 Å
I(0) (reciprocal space) i0_reciprocal	6517000.0000
Solution quality estimate total_estimate	0.7321
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.8 Å
Skewness Skewness skewness	0.074
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1096000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 0.287; Positv: 1.000; Valcen: 0.975; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	72 kDa type IV collagenase
Molecular weight formula_weight	17957.9 kDa
EC 编号 ec_number	3.4.24.24
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	1282

RKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWSLGKGVGYSLFLVAAHEFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASP

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 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1qiba_
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 (1 domains)

Domain ID domain_id	1qibA00
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	84.830 Å
Unit-cell length b length_b	84.830 Å
Unit-cell length c length_c	57.900 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	8

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2440

fit	/app/data/saxs_computation/qi/1qib/1qib.fit
pddf	/app/data/pr_computation/qi/1qib/1qib.pr.out
profile	/app/data/saxs_computation/qi/1qib/1qib.dat

CRYSTAL STRUCTURE OF GELATINASE A CATALYTIC DOMAIN

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

72 kDa type IV collagenase

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