SAXSdb — 3ayk

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

PROTEIN (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 101–269	Fragment：CATALYTIC FRAGMENT	ZN ZINC ION × 2 CA CALCIUM ION × 1 CGS N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE × 1	SOLUTION NMR NMR measurement conditions：pH 6.5；308 K；Pressure 1	Resolution not provided

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 3AYK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AYK INHIBITOR-FREE CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE, NMR, 30 STRUCTURES Deposited 1997-11-06	Different construct Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 101–269（169 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Pressure 1	Resolution not provided
1CGE CRYSTAL STRUCTURES OF RECOMBINANT 19-KDA HUMAN FIBROBLAST COLLAGENASE COMPLEXED TO ITSELF Deposited 1994-02-03	Different construct 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 102–269（168 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1CGF CRYSTAL STRUCTURES OF RECOMBINANT 19-KDA HUMAN FIBROBLAST COLLAGENASE COMPLEXED TO ITSELF Deposited 1994-02-03	Different construct 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 102–263（162 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1CGF CRYSTAL STRUCTURES OF RECOMBINANT 19-KDA HUMAN FIBROBLAST COLLAGENASE COMPLEXED TO ITSELF Deposited 1994-02-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 102–263（162 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1HFC 1.56 ANGSTROM STRUCTURE OF MATURE TRUNCATED HUMAN FIBROBLAST COLLAGENASE Deposited 1994-09-13	Different construct 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 101–269（169 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 PLH METHYLAMINO-PHENYLALANYL-LEUCYL-HYDROXAMIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1SU3 X-ray structure of human proMMP-1: New insights into collagenase action Deposited 2004-03-26	Different construct 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 20–469（450 aa）	Not recorded	CA CALCIUM ION × 4 CL CHLORIDE ION × 1 NA SODIUM ION × 1 ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；1.5M Li2SO4, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP	Resolution 2.20 Å R-free 0.252
1SU3 X-ray structure of human proMMP-1: New insights into collagenase action Deposited 2004-03-26	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–469（450 aa）	Not recorded	CA CALCIUM ION × 4 CL CHLORIDE ION × 1 NA SODIUM ION × 1 ZN ZINC ION × 2 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；1.5M Li2SO4, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP	Resolution 2.20 Å R-free 0.252
1SU3 X-ray structure of human proMMP-1: New insights into collagenase action Deposited 2004-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain B 20–469（450 aa）	Not recorded	CA CALCIUM ION × 32 CL CHLORIDE ION × 8 NA SODIUM ION × 8 ZN ZINC ION × 16 SO4 SULFATE ION × 32 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；1.5M Li2SO4, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP	Resolution 2.20 Å R-free 0.252
2AYK INHIBITOR-FREE CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-11-06	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 101–269（169 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 10 mM TRIS BASE, 100 mM NACL, 5 mM CACL2, 0.1 mM ZNCL2, 2mM NAN3, 10 mM DEUTERATED DTT, 90% H2O/10%D2O OR 100% D2O；Pressure 1	Resolution not provided
2CLT Crystal structure of the active form (full-length) of human fibroblast collagenase. Deposited 2006-04-29	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 100–466（367 aa）	Mutation：YES	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M TRIS (7.5); 10% PEG 8000; 1.5M AMMONIUM FORMATE, pH 7.50	Resolution 2.67 Å R-free 0.259
2CLT Crystal structure of the active form (full-length) of human fibroblast collagenase. Deposited 2006-04-29	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 100–466（367 aa）	Mutation：YES	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M TRIS (7.5); 10% PEG 8000; 1.5M AMMONIUM FORMATE, pH 7.50	Resolution 2.67 Å R-free 0.259
2J0T Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1 Deposited 2006-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 101–269（169 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 101-269	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).	Resolution 2.54 Å R-free 0.275
2J0T Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1 Deposited 2006-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 101–269（169 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 101-269	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).	Resolution 2.54 Å R-free 0.275
2J0T Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1 Deposited 2006-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 101–269（169 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 101-269	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).	Resolution 2.54 Å R-free 0.275
2TCL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST COLLAGENASE COMPLEXED WITH AN INHIBITOR Deposited 1994-09-07	Different construct 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 101–269（169 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 2 SM SAMARIUM (III) ION × 1 CA CALCIUM ION × 2 RO4 [[1-[N-HYDROXY-ACETAMIDYL]-3-METHYL-BUTYL]-CARBONYL-LEUCINYL]-ALANINE ETHYL ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
3SHI Crystal structure of human MMP1 catalytic domain at 2.2 A resolution Deposited 2011-06-16	Different construct 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 106–261（156 aa） Fragment：UNP residues 106-261	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；30% PEG8000, 0.1 M Tris-HCl, pH 8.5	Resolution 2.20 Å R-free 0.278
3SHI Crystal structure of human MMP1 catalytic domain at 2.2 A resolution Deposited 2011-06-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 106–261（156 aa） Fragment：UNP residues 106-261	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；30% PEG8000, 0.1 M Tris-HCl, pH 8.5	Resolution 2.20 Å R-free 0.278
3SHI Crystal structure of human MMP1 catalytic domain at 2.2 A resolution Deposited 2011-06-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain M 106–261（156 aa） Fragment：UNP residues 106-261	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；30% PEG8000, 0.1 M Tris-HCl, pH 8.5	Resolution 2.20 Å R-free 0.278
4AUO Crystal structure of MMP-1(E200A) in complex with a triple-helical collagen peptide Deposited 2012-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 100–466（367 aa）	Mutation：YES	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8	Resolution 3.00 Å R-free 0.273
4AUO Crystal structure of MMP-1(E200A) in complex with a triple-helical collagen peptide Deposited 2012-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 100–466（367 aa）	Mutation：YES	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8	Resolution 3.00 Å R-free 0.273
4AYK CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE COMPLEXED WITH CGS-27023A, NMR, 30 STRUCTURES Deposited 1999-02-01	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 101–269（169 aa） Fragment：CATALYTIC FRAGMENT	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 CGS N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE × 1	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Pressure 1	Resolution not provided
966C CRYSTAL STRUCTURE OF FIBROBLAST COLLAGENASE-1 COMPLEXED TO A DIPHENYL-ETHER SULPHONE BASED HYDROXAMIC ACID Deposited 1998-08-07	Different construct 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 108–264（157 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3 RS2 N-HYDROXY-2-[4-(4-PHENOXY-BENZENESULFONYL)-TETRAHYDRO-PYRAN-4-YL]-ACETAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.90 Å R-free 0.330

13 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MMP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 101–269

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	3ayk
Deposition date deposition_date	1999-02-01
Structure title title	CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE COMPLEXED WITH CGS-27023A, NMR, MINIMIZED AVERAGE STRUCTURE
Keywords keywords	MATRIX METALLOPROTEINASE, HYDROLASE, METALLOPROTEASE, GLYCOPROTEIN; MATRIX METALLOPROTEINASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.64 Å
Radius of gyration Rg (electron density) rg_electron	15.22 Å
Forward intensity I(0) i0	7037100.00
Molecular weight molecular_weight	18103.0 kDa
Excluded volume excluded_volume	22117 Å³
Envelope volume envelope_volume	26986 Å³
Hydration-shell volume shell_volume	14813 Å³
Envelope diameter envelope_diameter	50.4 Å
Shell Rg shell_rg	21.28 Å
Envelope Rg envelope_rg	15.42 Å
Shape Rg shape_rg	15.22 Å
Total Rg total_rg	16.36 Å
Total atoms total_atoms	2438
Residues n_residues	157
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	51.1 Å
Rg (real space) rg_real	16.49 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	7.0370e+06
I(0) uncertainty (real space) i0_real_error	7.8370e+04
Rg (reciprocal space) rg_reciprocal	16.51 Å
I(0) (reciprocal space) i0_reciprocal	7037000.0000
Solution quality estimate total_estimate	0.8970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.082
Kurtosis Kurtosis kurtosis	-0.421
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1491000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.991

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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	PROTEIN (COLLAGENASE)
Molecular weight formula_weight	18865.5 kDa
EC 编号 ec_number	3.4.24.7
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	2438

VLTEGNPRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRSQNPVQP

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	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	1

Entity 4 Entity 4 non-polymer

Description description	N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE
Molecular weight formula_weight	393.5 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ayka_
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	3aykA00
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 (3)

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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	1

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

fit	/app/data/saxs_computation/ay/3ayk/3ayk.fit
pddf	/app/data/pr_computation/ay/3ayk/3ayk.pr.out
profile	/app/data/saxs_computation/ay/3ayk/3ayk.dat

CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE COMPLEXED WITH CGS-27023A, NMR, MINIMIZED AVERAGE STRUCTURE