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1su3

X-ray structure of human proMMP-1: New insights into collagenase action

Method: X-RAY DIFFRACTION Dmax: 141.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Interstitial collagenase

Homo sapiens

UniProt P03956

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 20–469 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 20–469 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
3 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 20–469 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

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 1SU3 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 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 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 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 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 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 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
2AYK INHIBITOR-FREE CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-11-06 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 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 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 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 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 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 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 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
3AYK CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE COMPLEXED WITH CGS-27023A, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1999-02-01 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 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
3SHI Crystal structure of human MMP1 catalytic domain at 2.2 A resolution Deposited 2011-06-16 Different construct Different ligand/ion 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 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 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 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 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 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 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 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 20 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 1–450； UniProt 20–469 Author chain B； PDBConstruct 1–450； UniProt 20–469

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1su3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1su3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1su3
Deposition date deposition_date2004-03-26
Structure title titleX-ray structure of human proMMP-1: New insights into collagenase action
Keywords keywordsProdomain, Hemopexin domain, exocite, Structural Proteomics in Europe, SPINE, Structural Genomics, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.79 Å
Radius of gyration Rg (electron density) rg_electron44.25 Å
Forward intensity I(0) i0137261000.00
Molecular weight molecular_weight95479.0 kDa
Excluded volume excluded_volume119030 ų
Envelope volume envelope_volume163880 ų
Hydration-shell volume shell_volume34248 ų
Envelope diameter envelope_diameter150.7 Å
Shell Rg shell_rg42.62 Å
Envelope Rg envelope_rg43.36 Å
Shape Rg shape_rg44.20 Å
Total Rg total_rg44.33 Å
Total atoms total_atoms6727
Residues n_residues831
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax141.0 Å
Rg (real space) rg_real44.42 Å
Rg uncertainty (real space) rg_real_error1.73 Å
I(0) (real space) i0_real1.3730e+08
I(0) uncertainty (real space) i0_real_error2.5240e+06
Rg (reciprocal space) rg_reciprocal43.80 Å
I(0) (reciprocal space) i0_reciprocal137200000.0000
Solution quality estimate total_estimate0.7105
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.4 Å
Skewness Skewness skewness0.504
Kurtosis Kurtosis kurtosis-0.644
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6956000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.618; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.374; Smooth: 0.006
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1su3a1
Class classa — All alpha proteins
Fold Fold folda.20 — PGBD-like
Superfamily Superfamily superfamilya.20.1 — PGBD-like
Family Family familya.20.1.2 — MMP N-terminal domain
Domain ID domain_idd1su3a2
Class classb — All beta proteins
Fold Fold foldb.66 — 4-bladed beta-propeller
Superfamily Superfamily superfamilyb.66.1 — Hemopexin-like domain
Family Family familyb.66.1.1 — Hemopexin-like domain
Domain ID domain_idd1su3a3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.11 — Matrix metalloproteases, catalytic domain
Domain ID domain_idd1su3b1
Class classa — All alpha proteins
Fold Fold folda.20 — PGBD-like
Superfamily Superfamily superfamilya.20.1 — PGBD-like
Family Family familya.20.1.2 — MMP N-terminal domain
Domain ID domain_idd1su3b2
Class classb — All beta proteins
Fold Fold foldb.66 — 4-bladed beta-propeller
Superfamily Superfamily superfamilyb.66.1 — Hemopexin-like domain
Family Family familyb.66.1.1 — Hemopexin-like domain
Domain ID domain_idd1su3b3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id1su3A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1su3A02
Class class2 — Mainly Beta
Architecture architecture110 — 4 Propeller
Topology topology10 — Hemopexin
Homologous superfamily homologous superfamily10 — Hemopexin-like domain
Domain ID domain_id1su3B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1su3B02
Class class2 — Mainly Beta
Architecture architecture110 — 4 Propeller
Topology topology10 — Hemopexin
Homologous superfamily homologous superfamily10 — Hemopexin-like domain
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8. Citations (1)

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9. Files and Curves (10)