Collagenase 3
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 103–274 | Fragment：catalytic domain, residues 103-274 | ZN ZINC ION × 2 CA CALCIUM ION × 3 WNN 4-oxo-N-{3-[2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy]benzyl}-3,4-dihydroquinazoline-2-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM TrisHCl, 1000mM ammonium formate, 15.3% PEG8000 | Resolution 1.60 Å R-free 0.208 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 103–274 | Fragment：catalytic domain, residues 103-274 | ZN ZINC ION × 2 CA CALCIUM ION × 3 WNN 4-oxo-N-{3-[2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy]benzyl}-3,4-dihydroquinazoline-2-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM TrisHCl, 1000mM ammonium formate, 15.3% PEG8000 | Resolution 1.60 Å R-free 0.208 |
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 5B5P | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1EUB SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR Deposited 2000-04-14 | 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
104–274（171 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 HAV HYDROXYAMINOVALINE × 1 3MP 3-METHYLPYRIDINE × 1 MSB 1-METHYLOXY-4-SULFONE-BENZENE × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.8；310 K；Ionic strength (raw mmCIF value) 100 mM NACL；Pressure AMBIENT
NMR sample composition
0.5 MM COLLAGENASE-3 15N, 13C, 20 MM TRIS D11, 20 MM CACL2, 0.02% NAN3, 5 MM DTT, 100 MM NACL, 0.1 MM ZNCL,
|
Resolution not provided |
| 1FLS SOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED WITH A HYDROXAMIC ACID INHIBITOR Deposited 2000-08-15 | 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
104–268（165 aa）
Fragment：CATALYTIC FRAGMENT
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 WAY N-HYDROXY-2-[(4-METHOXY-BENZENESULFONYL)-PYRIDIN-3-YLMETHYL-AMINO]-3-METHYL-BENZAMIDE × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；308 K；Ionic strength (raw mmCIF value) 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT；Pressure ambient
NMR sample composition
1mM U-15N,13C-labeled MMP-13 with WAY-151693 in a 1:1 ratio,10mM deuterated Tris-Base, 100mM NaCl, 5mM CaCl2, 0.1mM ZnCl2, 2mM NaN3, 10mM deuterated DTT in 100% D2O at pH 6.5 and 35C. | 100% D2O
NMR sample composition
1mM U-15N,13C-labeled MMP-13 with WAY-151693 in a 1:1 ratio,10mM deuterated Tris-Base, 100mM NaCl, 5mM CaCl2, 0.1mM ZnCl2, 2mM NaN3, 10mM deuterated DTT in 90% H2O, 10% D2O at pH 6.5 and 35C. | 90% H2O/10% D2O
NMR sample composition
1mM U-15N-labeled MMP-13 with WAY-151693 in a 1:1 ratio,10mM deuterated Tris-Base, 100mM NaCl, 5mM CaCl2, 0.1mM ZnCl2, 2mM NaN3, 10mM deuterated DTT in 90% H2O, 10% D2O at pH 6.5 and 35C. | 90% H2O/10% D2O
|
Resolution not provided |
| 1FM1 SOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED WITH A HYDROXAMIC ACID INHIBITOR Deposited 2000-08-15 | 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
104–268（165 aa）
Fragment：CATALYTIC FRAGMENT
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 WAY N-HYDROXY-2-[(4-METHOXY-BENZENESULFONYL)-PYRIDIN-3-YLMETHYL-AMINO]-3-METHYL-BENZAMIDE × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；308 K；Ionic strength (raw mmCIF value) 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT；Pressure ambient
NMR sample composition
1 mM of U-15N,13C MMP-13 in an equimolar complex with WAY-151693 in a buffer containing 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT, in 100% D2O at pH 6.5 and 35C | 100% D2O
NMR sample composition
1 mM of U-15N,13C MMP-13 in an equimolar complex with WAY-151693 in a buffer containing 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT, in 90% H2O, 10% D2O at pH 6.5 and 35C | 90% H2O/10% D2O
NMR sample composition
1 mM of U-15N MMP-13 in an equimolar complex with WAY-151693 in a buffer containing 10 mM deuterated Tris-Base, 100 mM NaCl, 5 mM CaCl2, 0.1 mM ZnCl2, 2 mM NaN3, 10 mM deuterated DTT, in 90% H2O, 10% D2O at pH 6.5 and 35C | 90% H2O/10% D2O
|
Resolution not provided |
| 1PEX COLLAGENASE-3 (MMP-13) C-TERMINAL HEMOPEXIN-LIKE DOMAIN Deposited 1996-05-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
265–471（207 aa）
Fragment：C-TERMINAL HEMOPEXIN-LIKE DOMAIN
|
Not recorded | SO4 SULFATE ION × 1 CL CHLORIDE ION × 2 CA CALCIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.70 Å |
| 1XUC Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor Deposited 2004-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 PB3 N,N'-BIS(3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.70 Å R-free 0.200 |
| 1XUC Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor Deposited 2004-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 PB3 N,N'-BIS(3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.70 Å R-free 0.200 |
| 1XUD Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor Deposited 2004-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 PB4 N,N'-BIS(4-FLUORO-3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.203 |
| 1XUD Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor Deposited 2004-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 PB4 N,N'-BIS(4-FLUORO-3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.203 |
| 1XUR Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor Deposited 2004-10-26 | 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
104–274（171 aa）
Fragment：Catalytic domain
Chain B
104–274（171 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 4 PB5 N,N'-BIS(PYRIDIN-3-YLMETHYL)PYRIMIDINE-4,6-DICARBOXAMIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.85 Å R-free 0.206 |
| 1XUR Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor Deposited 2004-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–274（171 aa）
Fragment：Catalytic domain
Chain B
104–274（171 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 8 PB5 N,N'-BIS(PYRIDIN-3-YLMETHYL)PYRIMIDINE-4,6-DICARBOXAMIDE × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.85 Å R-free 0.206 |
| 1YOU Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor Deposited 2005-01-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–271（168 aa）
Fragment：MMP-13 catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 2 PFD 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.30 Å R-free 0.295 |
| 1YOU Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor Deposited 2005-01-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–271（168 aa）
Fragment：MMP-13 catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 1 PFD 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.30 Å R-free 0.295 |
| 1YOU Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor Deposited 2005-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–271（168 aa）
Fragment：MMP-13 catalytic domain
Chain B
104–271（168 aa）
Fragment：MMP-13 catalytic domain
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 4 SO4 SULFATE ION × 6 PFD 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.30 Å R-free 0.295 |
| 1ZTQ Crystal structure of the catalytic domain of MMP-13 complexed with WAY-033 Deposited 2005-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–268（165 aa）
Fragment：MMP-13 CATALYTIC DOMAIN
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 033 N-({4'-[(1-BENZOFURAN-2-YLCARBONYL)AMINO]-1,1'-BIPHENYL-4-YL}SULFONYL)-L-VALINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；20% PEG3350, 0.15M Ammonium Sulfate, 0.1M tris pH 8.5, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.287 |
| 1ZTQ Crystal structure of the catalytic domain of MMP-13 complexed with WAY-033 Deposited 2005-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–268（165 aa）
Fragment：MMP-13 CATALYTIC DOMAIN
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 033 N-({4'-[(1-BENZOFURAN-2-YLCARBONYL)AMINO]-1,1'-BIPHENYL-4-YL}SULFONYL)-L-VALINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；20% PEG3350, 0.15M Ammonium Sulfate, 0.1M tris pH 8.5, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.287 |
| 1ZTQ Crystal structure of the catalytic domain of MMP-13 complexed with WAY-033 Deposited 2005-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
104–268（165 aa）
Fragment：MMP-13 CATALYTIC DOMAIN
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 033 N-({4'-[(1-BENZOFURAN-2-YLCARBONYL)AMINO]-1,1'-BIPHENYL-4-YL}SULFONYL)-L-VALINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；20% PEG3350, 0.15M Ammonium Sulfate, 0.1M tris pH 8.5, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.287 |
| 1ZTQ Crystal structure of the catalytic domain of MMP-13 complexed with WAY-033 Deposited 2005-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
104–268（165 aa）
Fragment：MMP-13 CATALYTIC DOMAIN
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 033 N-({4'-[(1-BENZOFURAN-2-YLCARBONYL)AMINO]-1,1'-BIPHENYL-4-YL}SULFONYL)-L-VALINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；20% PEG3350, 0.15M Ammonium Sulfate, 0.1M tris pH 8.5, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.287 |
| 2D1N Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor Deposited 2005-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–269（166 aa）
Fragment：C-Terminal catalytic domain
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 3 FA4 SM-25453 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；potassium sodium tartrate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.37 Å R-free 0.239 |
| 2D1N Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor Deposited 2005-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–269（166 aa）
Fragment：C-Terminal catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 FA4 SM-25453 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；potassium sodium tartrate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.37 Å R-free 0.239 |
| 2E2D Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2 Deposited 2006-11-11 | 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
104–268（165 aa）
Fragment：catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM MES, 200 mM magnesium acetate, 20 % PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.231 |
| 2OW9 Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor Deposited 2007-02-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–270（167 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 SO4 SULFATE ION × 1 SP6 BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE × 1 HAE ACETOHYDROXAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Protein concentration: 7-20 mg/ml. Well solution: 18-22% PEG MME 5000, 0.2M Lithium sulfate, 0.1M Hepes buffer. 2-4 microliter drops with 1:1 ratio of protein complex solution and well solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.74 Å R-free 0.191 |
| 2OW9 Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor Deposited 2007-02-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–270（167 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 4 SP6 BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE × 1 HAE ACETOHYDROXAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Protein concentration: 7-20 mg/ml. Well solution: 18-22% PEG MME 5000, 0.2M Lithium sulfate, 0.1M Hepes buffer. 2-4 microliter drops with 1:1 ratio of protein complex solution and well solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.74 Å R-free 0.191 |
| 2OW9 Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor Deposited 2007-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–270（167 aa）
Fragment：Catalytic domain
Chain B
104–270（167 aa）
Fragment：Catalytic domain
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 14 SO4 SULFATE ION × 2 SP6 BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE × 4 HAE ACETOHYDROXAMIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Protein concentration: 7-20 mg/ml. Well solution: 18-22% PEG MME 5000, 0.2M Lithium sulfate, 0.1M Hepes buffer. 2-4 microliter drops with 1:1 ratio of protein complex solution and well solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.74 Å R-free 0.191 |
| 2OZR MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid Deposited 2007-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
104–270（167 aa）
Fragment：Catalytic Domain
Chain B
104–270（167 aa）
Fragment：Catalytic Domain
Chain C
104–270（167 aa）
Fragment：Catalytic Domain
Chain D
104–270（167 aa）
Fragment：Catalytic Domain
Chain E
104–270（167 aa）
Fragment：Catalytic Domain
Chain F
104–270（167 aa）
Fragment：Catalytic Domain
Chain G
104–270（167 aa）
Fragment：Catalytic Domain
Chain H
104–270（167 aa）
Fragment：Catalytic Domain
|
Not recorded | ZN ZINC ION × 16 CA CALCIUM ION × 24 GG1 4-{[1-METHYL-2,4-DIOXO-6-(3-PHENYLPROP-1-YN-1-YL)-1,4-DIHYDROQUINAZOLIN-3(2H)-YL]METHYL}BENZOIC ACID × 8 HAE ACETOHYDROXAMIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Dissolved in DMSO inhibitor was mixed with protein (protein concentration: 1mg/ml) at 5:1 ratio, 0.1 M acetohydrohamic acid added. Ternary complex was concentrated (to 17 mg/ml protien concentration). 1-2 uL hagind drops were mixed with same amount of reservoit solution (2.1 M ammonium sulfate in 0.1 M Hepes buffer) , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.340 |
| 2PJT Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344 Deposited 2007-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–268（165 aa）
Fragment：Catalytic domain: Residues 104-268
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 347 TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAMINO)PHENYL]SULFONYL}METHYL)-4-[(HYDROXYAMINO)CARBONYL]PIPERIDINE-1-CARBOXYLATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；20% PEG 3350, 0.2M MgCl2, 0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 2.80 Å R-free 0.270 |
| 2PJT Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344 Deposited 2007-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–268（165 aa）
Fragment：Catalytic domain: Residues 104-268
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 347 TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAMINO)PHENYL]SULFONYL}METHYL)-4-[(HYDROXYAMINO)CARBONYL]PIPERIDINE-1-CARBOXYLATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；20% PEG 3350, 0.2M MgCl2, 0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 2.80 Å R-free 0.270 |
| 2PJT Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344 Deposited 2007-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
104–268（165 aa）
Fragment：Catalytic domain: Residues 104-268
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 347 TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAMINO)PHENYL]SULFONYL}METHYL)-4-[(HYDROXYAMINO)CARBONYL]PIPERIDINE-1-CARBOXYLATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；20% PEG 3350, 0.2M MgCl2, 0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 2.80 Å R-free 0.270 |
| 2PJT Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344 Deposited 2007-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
104–268（165 aa）
Fragment：Catalytic domain: Residues 104-268
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 347 TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAMINO)PHENYL]SULFONYL}METHYL)-4-[(HYDROXYAMINO)CARBONYL]PIPERIDINE-1-CARBOXYLATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；20% PEG 3350, 0.2M MgCl2, 0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 2.80 Å R-free 0.270 |
| 2YIG MMP13 in complex with a novel selective non zinc binding inhibitor Deposited 2011-05-13 | 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
104–274（171 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 104-274
Chain B
104–274（171 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 104-274
|
Not recorded | 5EL 4-(4-{[(3S)-3-HYDROXY-1-AZABICYCLO[2.2.2]OCT-3-YL]ETHYNYL}PHENOXY)-N-(PYRIDIN-4-YLMETHYL)BENZAMIDE × 2 ZN ZINC ION × 4 CA CALCIUM ION × 4 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
10-27% PEG 3350, 1.5 M AMMONIUM FORMATE, 0.1 M TRIS/HCL PH 8.5
|
Resolution 1.70 Å R-free 0.221 |
| 3ELM Crystal Structure of MMP-13 Complexed with Inhibitor 24f Deposited 2008-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–274（171 aa）
Fragment：UNP residues 104 to 274
Chain B
104–274（171 aa）
Fragment：UNP residues 104 to 274
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 14 24F (2R)-({[5-(4-ethoxyphenyl)thiophen-2-yl]sulfonyl}amino){1-[(1-methylethoxy)carbonyl]piperidin-4-yl}ethanoic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；278 K；13% PEG 6K, 0.1M Tris, 1.2M NaAcetate, 2% glycerol, 15 mM CaCl2, 10 uM Zn(Ac)2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 1.90 Å R-free 0.202 |
| 3ELM Crystal Structure of MMP-13 Complexed with Inhibitor 24f Deposited 2008-09-22 | 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 A
104–274（171 aa）
Fragment：UNP residues 104 to 274
Chain B
104–274（171 aa）
Fragment：UNP residues 104 to 274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 7 24F (2R)-({[5-(4-ethoxyphenyl)thiophen-2-yl]sulfonyl}amino){1-[(1-methylethoxy)carbonyl]piperidin-4-yl}ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；278 K；13% PEG 6K, 0.1M Tris, 1.2M NaAcetate, 2% glycerol, 15 mM CaCl2, 10 uM Zn(Ac)2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 1.90 Å R-free 0.202 |
| 3I7G MMP-13 in complex with a non zinc-chelating inhibitor Deposited 2009-07-08 | 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
104–274（171 aa）
Fragment：UNP residues 104-274
Chain B
104–274（171 aa）
Fragment：UNP residues 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 6 FMT FORMIC ACID × 2 732 5-(4-chlorophenyl)-N-[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]furan-2-carboxamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.228 |
| 3I7G MMP-13 in complex with a non zinc-chelating inhibitor Deposited 2009-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–274（171 aa）
Fragment：UNP residues 104-274
Chain B
104–274（171 aa）
Fragment：UNP residues 104-274
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 12 FMT FORMIC ACID × 4 732 5-(4-chlorophenyl)-N-[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]furan-2-carboxamide × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.228 |
| 3I7I MMP-13 in complex with a non zinc-chelating inhibitor Deposited 2009-07-08 | 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
104–274（171 aa）
Fragment：UNP residues 104-274
Chain B
104–274（171 aa）
Fragment：UNP residues 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 6 518 N-[4-(5-{[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]carbamoyl}furan-2-yl)phenyl]-1-benzofuran-2-carboxamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.21 Å R-free 0.314 |
| 3I7I MMP-13 in complex with a non zinc-chelating inhibitor Deposited 2009-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–274（171 aa）
Fragment：UNP residues 104-274
Chain B
104–274（171 aa）
Fragment：UNP residues 104-274
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 12 518 N-[4-(5-{[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]carbamoyl}furan-2-yl)phenyl]-1-benzofuran-2-carboxamide × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.21 Å R-free 0.314 |
| 3KEC Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound Deposited 2009-10-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
105–267（163 aa）
Fragment：catalytic domain, UNP residues 104-270
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 SO4 SULFATE ION × 2 3KE 4-{[({3-[2-(4-methoxybenzyl)-2H-tetrazol-5-yl]phenyl}carbonyl)amino]methyl}benzoic acid × 1 HAE ACETOHYDROXAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2
reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2
drop ratio: 5ul protein + 1 ul reservoir, Vapor diffusion, sitting drop, temperature 277K
|
Resolution 2.05 Å R-free 0.204 |
| 3KEC Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound Deposited 2009-10-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
105–267（163 aa）
Fragment：catalytic domain, UNP residues 104-270
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 3KE 4-{[({3-[2-(4-methoxybenzyl)-2H-tetrazol-5-yl]phenyl}carbonyl)amino]methyl}benzoic acid × 1 HAE ACETOHYDROXAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2
reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2
drop ratio: 5ul protein + 1 ul reservoir, Vapor diffusion, sitting drop, temperature 277K
|
Resolution 2.05 Å R-free 0.204 |
| 3KEJ Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound Deposited 2009-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–270（167 aa）
Fragment：catalytic domain, UNP residues 104-270
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 3EJ 4-[(5-{2-[(3-fluorobenzyl)carbamoyl]pyridin-4-yl}-2H-tetrazol-2-yl)methyl]benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2.
reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2.
drop ratio: 5ul protein + 1 ul
reservoir., VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.236 |
| 3KEJ Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound Deposited 2009-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–270（167 aa）
Fragment：catalytic domain, UNP residues 104-270
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 3EJ 4-[(5-{2-[(3-fluorobenzyl)carbamoyl]pyridin-4-yl}-2H-tetrazol-2-yl)methyl]benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2.
reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2.
drop ratio: 5ul protein + 1 ul
reservoir., VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.236 |
| 3KEK Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound Deposited 2009-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
105–271（167 aa）
Fragment：catalytic domain, UNP residues 104-270
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 3EK trans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2.
reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2.
drop ratio: 5ul protein + 1 ul
reservoir., VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.97 Å R-free 0.218 |
| 3KEK Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound Deposited 2009-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
105–271（167 aa）
Fragment：catalytic domain, UNP residues 104-270
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 3EK trans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2.
reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2.
drop ratio: 5ul protein + 1 ul
reservoir., VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.97 Å R-free 0.218 |
| 3KRY Crystal structure of MMP-13 in complex with SC-78080 Deposited 2009-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 3KR 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；100mM Hepes buffer, pH 7.4
1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.256 |
| 3KRY Crystal structure of MMP-13 in complex with SC-78080 Deposited 2009-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 3KR 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；100mM Hepes buffer, pH 7.4
1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.256 |
| 3KRY Crystal structure of MMP-13 in complex with SC-78080 Deposited 2009-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 3KR 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；100mM Hepes buffer, pH 7.4
1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.256 |
| 3KRY Crystal structure of MMP-13 in complex with SC-78080 Deposited 2009-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 3KR 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；100mM Hepes buffer, pH 7.4
1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.256 |
| 3KRY Crystal structure of MMP-13 in complex with SC-78080 Deposited 2009-11-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
Chain B
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
Chain C
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
Chain D
104–267（164 aa）
Fragment：catalytic domain, residues 104-267
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 8 3KR 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；100mM Hepes buffer, pH 7.4
1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.256 |
| 3LJZ Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound Deposited 2010-01-26 | 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
105–267（163 aa）
Fragment：UNP residues 104-267
|
Mutation：Y104A | CA CALCIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 2 LA3 (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2. reservoir:
1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2. drop ratio: 5ul protein + 1 ul reservoir. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.228 |
| 3LJZ Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound Deposited 2010-01-26 | 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
105–267（163 aa）
Fragment：UNP residues 104-267
|
Mutation：Y104A | CA CALCIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 2 LA3 (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2. reservoir:
1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2. drop ratio: 5ul protein + 1 ul reservoir. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.228 |
| 3LJZ Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound Deposited 2010-01-26 | 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
105–267（163 aa）
Fragment：UNP residues 104-267
|
Mutation：Y104A | CA CALCIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 2 LA3 (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2. reservoir:
1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2. drop ratio: 5ul protein + 1 ul reservoir. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.228 |
| 3LJZ Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound Deposited 2010-01-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
105–267（163 aa）
Fragment：UNP residues 104-267
|
Mutation：Y104A | CA CALCIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 3 LA3 (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2. reservoir:
1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2. drop ratio: 5ul protein + 1 ul reservoir. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.228 |
| 3O2X MMP-13 in complex with selective tetrazole core inhibitor Deposited 2010-07-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
105–267（163 aa）
Fragment：Catalytic domain
|
Not recorded | 3O2 N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide × 1 ZN ZINC ION × 2 CA CALCIUM ION × 2 SO4 SULFATE ION × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.210 |
| 3O2X MMP-13 in complex with selective tetrazole core inhibitor Deposited 2010-07-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
105–267（163 aa）
Fragment：Catalytic domain
|
Not recorded | 3O2 N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide × 1 ZN ZINC ION × 2 CA CALCIUM ION × 2 SO4 SULFATE ION × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.210 |
| 3O2X MMP-13 in complex with selective tetrazole core inhibitor Deposited 2010-07-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
105–267（163 aa）
Fragment：Catalytic domain
|
Not recorded | 3O2 N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide × 1 ZN ZINC ION × 2 CA CALCIUM ION × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.210 |
| 3O2X MMP-13 in complex with selective tetrazole core inhibitor Deposited 2010-07-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
105–267（163 aa）
Fragment：Catalytic domain
|
Not recorded | 3O2 N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide × 1 ZN ZINC ION × 2 CA CALCIUM ION × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.210 |
| 3O2X MMP-13 in complex with selective tetrazole core inhibitor Deposited 2010-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
105–267（163 aa）
Fragment：Catalytic domain
Chain B
105–267（163 aa）
Fragment：Catalytic domain
Chain C
105–267（163 aa）
Fragment：Catalytic domain
Chain D
105–267（163 aa）
Fragment：Catalytic domain
|
Not recorded | 3O2 N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide × 4 ZN ZINC ION × 8 CA CALCIUM ION × 8 SO4 SULFATE ION × 9 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.210 |
| 3O2X MMP-13 in complex with selective tetrazole core inhibitor Deposited 2010-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
105–267（163 aa）
Fragment：Catalytic domain
Chain C
105–267（163 aa）
Fragment：Catalytic domain
|
Not recorded | 3O2 N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide × 2 ZN ZINC ION × 4 CA CALCIUM ION × 4 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.210 |
| 3O2X MMP-13 in complex with selective tetrazole core inhibitor Deposited 2010-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
105–267（163 aa）
Fragment：Catalytic domain
Chain D
105–267（163 aa）
Fragment：Catalytic domain
|
Not recorded | 3O2 N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide × 2 ZN ZINC ION × 4 CA CALCIUM ION × 4 SO4 SULFATE ION × 5 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.210 |
| 3TVC Human MMP13 in complex with L-glutamate motif inhibitor Deposited 2011-09-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–272（169 aa）
Fragment：MMP-13 catalytic subunit (UNP residues 104-272)
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 E3P N~2~-[3-(1,1':4',1''-terphenyl-4-yl)propanoyl]-L-alpha-glutamine × 1 PEG DI(HYDROXYETHYL)ETHER × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PROTEIN-INHIBITOR SOLUTION: MMP13 AT 20 MG/ML CO-CRYSTALLIZED WITH E3P AT 1.1 MILLI-M. RESERVOIR SOLUTION: 17.5% PEG 20K, 0.1 M MES, 0.02 M NACL. CRYOPROTECTANT: 5% DIETHYLENE GLYCOL, 5% ETHYLENE GLYCOL, 5% MPD, 5% PROPYLENE GLYCOL, 5% DMSO, 5% GLYCEROL, 0.005 M 3-(-PYRIDINIO)-1-PROPANESULFONATE, 10% PEG 20K, 0.033 M SODIUM ACETATE, 0.033 M ADA, 0.033 M BICINE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
|
Resolution 2.43 Å R-free 0.234 |
| 3WV1 Crystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid Deposited 2014-05-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 FMT FORMIC ACID × 1 WHH 4-[2-({6-fluoro-2-[(3-methoxybenzyl)carbamoyl]-4-oxo-3,4-dihydroquinazolin-5-yl}oxy)ethyl]benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；8-16%(w/v) PEG8000, 1.0-1.5M ammonium formate, 0.1M Tris HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.98 Å R-free 0.220 |
| 3WV1 Crystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid Deposited 2014-05-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 FMT FORMIC ACID × 1 WHH 4-[2-({6-fluoro-2-[(3-methoxybenzyl)carbamoyl]-4-oxo-3,4-dihydroquinazolin-5-yl}oxy)ethyl]benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；8-16%(w/v) PEG8000, 1.0-1.5M ammonium formate, 0.1M Tris HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.98 Å R-free 0.220 |
| 3WV1 Crystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid Deposited 2014-05-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
Chain B
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 4 NA SODIUM ION × 2 FMT FORMIC ACID × 2 WHH 4-[2-({6-fluoro-2-[(3-methoxybenzyl)carbamoyl]-4-oxo-3,4-dihydroquinazolin-5-yl}oxy)ethyl]benzoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；8-16%(w/v) PEG8000, 1.0-1.5M ammonium formate, 0.1M Tris HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.98 Å R-free 0.220 |
| 3WV2 Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide Deposited 2014-05-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 WGG N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5uM Zn(OAc)2, 5mM CaCl2, 50mM NaCl, 20mM Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.241 |
| 3WV2 Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide Deposited 2014-05-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 WGG N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5uM Zn(OAc)2, 5mM CaCl2, 50mM NaCl, 20mM Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.241 |
| 3WV2 Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide Deposited 2014-05-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
Chain B
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 4 NA SODIUM ION × 2 WGG N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5uM Zn(OAc)2, 5mM CaCl2, 50mM NaCl, 20mM Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.241 |
| 3WV3 Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide Deposited 2014-05-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 FMT FORMIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 WLL N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100mM TrisHCl, 1500mM ammonium formate, 17.7% PEG8000, pH 8.5, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.60 Å R-free 0.212 |
| 3WV3 Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide Deposited 2014-05-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 FMT FORMIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 WLL N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100mM TrisHCl, 1500mM ammonium formate, 17.7% PEG8000, pH 8.5, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.60 Å R-free 0.212 |
| 3WV3 Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide Deposited 2014-05-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
Chain B
104–274（171 aa）
Fragment：catalytic domain, residues 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 4 NA SODIUM ION × 2 FMT FORMIC ACID × 2 EDO 1,2-ETHANEDIOL × 2 WLL N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100mM TrisHCl, 1500mM ammonium formate, 17.7% PEG8000, pH 8.5, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.60 Å R-free 0.212 |
| 3ZXH MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor Deposited 2011-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–274（171 aa）
Fragment：PROTEASE DOMAIN, RESIDUES 104-274
Chain B
104–274（171 aa）
Fragment：PROTEASE DOMAIN, RESIDUES 104-274
|
Not recorded | ZN ZINC ION × 8 CA CALCIUM ION × 14 E41 N-hydroxy-N^2^-(3-methylbutyl)-N^2^-(naphthalen-2-ylsulfonyl)-D-valinamide × 4 GOL GLYCEROL × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.2；277 K；15% PEG 6K, 0.1M TRIS PH 8.2, 0.9 M HCOONA, 4 DEG. CELSIUS.
|
Resolution 1.30 Å R-free 0.159 |
| 3ZXH MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor Deposited 2011-08-10 | 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 A
104–274（171 aa）
Fragment：PROTEASE DOMAIN, RESIDUES 104-274
Chain B
104–274（171 aa）
Fragment：PROTEASE DOMAIN, RESIDUES 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 7 E41 N-hydroxy-N^2^-(3-methylbutyl)-N^2^-(naphthalen-2-ylsulfonyl)-D-valinamide × 2 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.2；277 K；15% PEG 6K, 0.1M TRIS PH 8.2, 0.9 M HCOONA, 4 DEG. CELSIUS.
|
Resolution 1.30 Å R-free 0.159 |
| 456C CRYSTAL STRUCTURE OF COLLAGENASE-3 (MMP-13) COMPLEXED TO A DIPHENYL-ETHER SULPHONE BASED HYDROXAMIC ACID Deposited 1998-08-06 | 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
104–271（168 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 110-269
Chain B
104–271（168 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 110-269
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 2 CBP 2-{4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYL]-TETRAHYDRO-PYRAN-4-YL}-N-HYDROXY-ACETAMIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；pH 8.0
|
Resolution 2.40 Å R-free 0.338 |
| 4A7B MMP13 IN COMPLEX WITH A NOVEL SELECTIVE NON ZINC BINDING INHIBITOR CMPD22 Deposited 2011-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–272（169 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 104-272
Chain B
104–272（169 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 104-272
|
Not recorded | 3W5 N-[(3S)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide × 2 HAE ACETOHYDROXAMIC ACID × 4 GOL GLYCEROL × 4 ZN ZINC ION × 8 CA CALCIUM ION × 8 NA SODIUM ION × 4 3W4 N-[(3R)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；10-27% PEG 3350, 1.5 M AMMONIUM FORMATE, 0.1 M TRIS/HCL PH 8.5
|
Resolution 2.20 Å R-free 0.253 |
| 4FU4 Human collagenase 3 (MMP-13) with peptide from pro-domain Deposited 2012-06-28 | 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
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain C
25–50（26 aa）
Fragment：pro-domain fragment (UNP residues 25-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；PROPEPTIDE IMPURITY INDUCES CRYSTALLIZATION ON COLD STORAGE CRYOPROTECTANT: 20% MPEG2K, 10% MPEG550, 10% ethylene glycol, 90mM imidazole malate, pH 6.0, SLOW COOLING, temperature 277.0K
|
Resolution 2.85 Å R-free 0.247 |
| 4FU4 Human collagenase 3 (MMP-13) with peptide from pro-domain Deposited 2012-06-28 | 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
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain D
25–50（26 aa）
Fragment：pro-domain fragment (UNP residues 25-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；PROPEPTIDE IMPURITY INDUCES CRYSTALLIZATION ON COLD STORAGE CRYOPROTECTANT: 20% MPEG2K, 10% MPEG550, 10% ethylene glycol, 90mM imidazole malate, pH 6.0, SLOW COOLING, temperature 277.0K
|
Resolution 2.85 Å R-free 0.247 |
| 4FVL Human collagenase 3 (MMP-13) full form with peptides from pro-domain Deposited 2012-06-29 | 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
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain C
31–50（20 aa）
Fragment：pro-domain fragment (UNP residues 31-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 5 CL CHLORIDE ION × 2 GOL GLYCEROL × 3 PGO S-1,2-PROPANEDIOL × 16 PEG DI(HYDROXYETHYL)ETHER × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；propeptide impurity induces crystallization on cold storage cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 80/20, 0.2 M NaCl, pH 7.5, SLOW COOLING, temperature 277.0K
|
Resolution 2.44 Å R-free 0.223 |
| 4FVL Human collagenase 3 (MMP-13) full form with peptides from pro-domain Deposited 2012-06-29 | 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
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain D
31–50（20 aa）
Fragment：pro-domain fragment (UNP residues 31-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 5 CL CHLORIDE ION × 1 GOL GLYCEROL × 7 PGO S-1,2-PROPANEDIOL × 12 PEG DI(HYDROXYETHYL)ETHER × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；propeptide impurity induces crystallization on cold storage cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 80/20, 0.2 M NaCl, pH 7.5, SLOW COOLING, temperature 277.0K
|
Resolution 2.44 Å R-free 0.223 |
| 4G0D Human collagenase 3 (MMP-13) full form with peptides from pro-domain Deposited 2012-07-09 | 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
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain W
25–50（26 aa）
Fragment：pro-domain fragment (UNP residues 25-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 5 CL CHLORIDE ION × 1 PGO S-1,2-PROPANEDIOL × 11 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；propeptide impurity induces crystallization on cold storage Cryoprotectant: 10% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7.5, SLOW COOLING, temperature 277.0K
|
Resolution 2.54 Å R-free 0.241 |
| 4G0D Human collagenase 3 (MMP-13) full form with peptides from pro-domain Deposited 2012-07-09 | 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
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain X
25–50（26 aa）
Fragment：pro-domain fragment (UNP residues 25-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 6 CL CHLORIDE ION × 2 PGO S-1,2-PROPANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 3 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；propeptide impurity induces crystallization on cold storage Cryoprotectant: 10% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7.5, SLOW COOLING, temperature 277.0K
|
Resolution 2.54 Å R-free 0.241 |
| 4G0D Human collagenase 3 (MMP-13) full form with peptides from pro-domain Deposited 2012-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain Y
25–50（26 aa）
Fragment：pro-domain fragment (UNP residues 25-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 7 CL CHLORIDE ION × 2 PGO S-1,2-PROPANEDIOL × 11 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；propeptide impurity induces crystallization on cold storage Cryoprotectant: 10% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7.5, SLOW COOLING, temperature 277.0K
|
Resolution 2.54 Å R-free 0.241 |
| 4G0D Human collagenase 3 (MMP-13) full form with peptides from pro-domain Deposited 2012-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain D
104–471（368 aa）
Fragment：Inactive full form (UNP residues 104-471)
Chain Z
25–50（26 aa）
Fragment：pro-domain fragment (UNP residues 25-50)
|
Mutation：E223A | ZN ZINC ION × 2 CA CALCIUM ION × 5 CL CHLORIDE ION × 3 PGO S-1,2-PROPANEDIOL × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SLOW COOLING；pH 7.5；277 K；propeptide impurity induces crystallization on cold storage Cryoprotectant: 10% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7.5, SLOW COOLING, temperature 277.0K
|
Resolution 2.54 Å R-free 0.241 |
| 4JP4 Mmp13 in complex with a reverse hydroxamate Zn-binder Deposited 2013-03-19 | 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
103–274（172 aa）
Fragment：UNP RESIDUES 103-274
Chain B
103–274（172 aa）
Fragment：UNP RESIDUES 103-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 4 NA SODIUM ION × 2 AZ4 N-[(2S)-4-(5-fluoropyrimidin-2-yl)-1-({4-[5-(2,2,2-trifluoroethoxy)pyrimidin-2-yl]piperazin-1-yl}sulfonyl)butan-2-yl]-N-hydroxyformamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；27.5% PEG 4000, 1.25M AmFormate, 100mM TrisHCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 1.43 Å R-free 0.175 |
| 4JPA Mmp13 in complex with a piperazine hydantoin ligand Deposited 2013-03-19 | 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
103–274（172 aa）
Fragment：UNP RESIDUES 103-274
Chain B
103–274（172 aa）
Fragment：UNP RESIDUES 103-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 4 NA SODIUM ION × 2 AZ6 3-[({2-[4-({[(4S)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}sulfonyl)piperazin-1-yl]pyrimidin-5-yl}oxy)methyl]benzonitrile × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；27.5% PEG 4000 1.25M AmFormate, 100mM TrisHCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.00 Å R-free 0.230 |
| 4L19 Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1 Deposited 2013-06-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
Fragment：Catalytic domain (UNP residues 104-274)
|
Not recorded | ZN ZINC ION × 3 CA CALCIUM ION × 2 FMT FORMIC ACID × 1 1UA 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；277 K；0.1M Tris, 1.5M ammonium formate, 10%-14% PEG4000, 0.017M compound Q1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.66 Å R-free 0.199 |
| 4L19 Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1 Deposited 2013-06-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
Fragment：Catalytic domain (UNP residues 104-274)
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 FMT FORMIC ACID × 4 1UA 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；277 K；0.1M Tris, 1.5M ammonium formate, 10%-14% PEG4000, 0.017M compound Q1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.66 Å R-free 0.199 |
| 4L19 Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1 Deposited 2013-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
104–274（171 aa）
Fragment：Catalytic domain (UNP residues 104-274)
Chain B
104–274（171 aa）
Fragment：Catalytic domain (UNP residues 104-274)
|
Not recorded | ZN ZINC ION × 10 CA CALCIUM ION × 8 FMT FORMIC ACID × 10 1UA 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one × 6 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；277 K；0.1M Tris, 1.5M ammonium formate, 10%-14% PEG4000, 0.017M compound Q1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.66 Å R-free 0.199 |
| 5B5O Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine Deposited 2016-05-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
103–274（172 aa）
Fragment：catalytic domain, residues 103-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 WMM N-phenyl-4-[(4H-1,2,4-triazol-3-ylsulfanyl)methyl]-1,3-thiazol-2-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM TrisHCl, 1500mM ammonium formate, 10.4% PEG8000
|
Resolution 1.20 Å R-free 0.185 |
| 5B5O Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine Deposited 2016-05-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
103–274（172 aa）
Fragment：catalytic domain, residues 103-274
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 WMM N-phenyl-4-[(4H-1,2,4-triazol-3-ylsulfanyl)methyl]-1,3-thiazol-2-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM TrisHCl, 1500mM ammonium formate, 10.4% PEG8000
|
Resolution 1.20 Å R-free 0.185 |
| 5BOT X-RAY Co-structure of MMP-13 with ethyl 5-carbamoyl-1H-indole-2-carboxylate Deposited 2015-05-27 | 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
104–274（171 aa）
Fragment：UNP residues 104-274
Chain B
104–274（171 aa）
Fragment：UNP residues 104-274
|
Not recorded | 4UM ethyl 5-carbamoyl-1H-indole-2-carboxylate × 2 ZN ZINC ION × 4 CA CALCIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；14-28% PEG 4000 0.6M Ammonium Formate 0.
M Tris pH 8
|
Resolution 1.85 Å R-free 0.229 |
| 5BOY X-RAY Co-structure of MMP-13 with ethyl 5-(1-methyl-1H-imidazol-5-yl)-1H-indole-2-Carboxylate Deposited 2015-05-27 | 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
104–274（171 aa）
Fragment：UNP residues 104-274
Chain B
104–274（171 aa）
Fragment：UNP residues 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 6 4UE ethyl 5-(1-methyl-1H-imidazol-5-yl)-1H-indole-2-carboxylate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG 4000, 1M Ammonimum Formate, 100 mM Tris pH 8
|
Resolution 2.03 Å R-free 0.190 |
| 5BPA X-RAY Co-structure of MMP-13 with 4-[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}formamido)methyl]benzoate Deposited 2015-05-27 | 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
104–274（171 aa）
Fragment：UNP residues 104-274
Chain B
104–274（171 aa）
Fragment：UNP residues 104-274
|
Not recorded | ZN ZINC ION × 4 CA CALCIUM ION × 6 4UF 4-{[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}carbonyl)amino]methyl}benzoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；293 K；10% PEG4000, 1M Ammonium Formate, 100 mM Tris
|
Resolution 1.79 Å R-free 0.280 |
| 5UWK Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 8OM (S)-3-methyl-2-(4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-ylsulfonamido)butanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M magnesium chloride, 0.1 M Tris:HCl pH 8.5, 25% PEG 3350
|
Resolution 1.60 Å R-free 0.199 |
| 5UWK Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 8OM (S)-3-methyl-2-(4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-ylsulfonamido)butanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M magnesium chloride, 0.1 M Tris:HCl pH 8.5, 25% PEG 3350
|
Resolution 1.60 Å R-free 0.199 |
| 5UWL Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-17a Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 8OJ (S)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)phenyl)furan-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M sodium chloride, 0.1 M Tris pH 7, 1.0 M sodium citrate
|
Resolution 2.55 Å R-free 0.239 |
| 5UWL Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-17a Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 8OJ (S)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)phenyl)furan-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M sodium chloride, 0.1 M Tris pH 7, 1.0 M sodium citrate
|
Resolution 2.55 Å R-free 0.239 |
| 5UWM Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a Deposited 2017-02-21 | 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
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 8OA (R)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)phenyl)furan-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulfate 0.1 M Tris:HCl pH 8.5, 30% polyethylene glycol 4000
|
Resolution 1.62 Å R-free 0.178 |
| 5UWM Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a Deposited 2017-02-21 | 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
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 8OA (R)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)phenyl)furan-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulfate 0.1 M Tris:HCl pH 8.5, 30% polyethylene glycol 4000
|
Resolution 1.62 Å R-free 0.178 |
| 5UWN Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 8O7 N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonami de × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, 1.6 M ammonium sulfate
|
Resolution 3.20 Å R-free 0.234 |
| 5UWN Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 8O7 N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonami de × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, 1.6 M ammonium sulfate
|
Resolution 3.20 Å R-free 0.234 |
| 5UWN Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 8O7 N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonami de × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, 1.6 M ammonium sulfate
|
Resolution 3.20 Å R-free 0.234 |
| 5UWN Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 8O7 N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonami de × 1 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, 1.6 M ammonium sulfate
|
Resolution 3.20 Å R-free 0.234 |
| 5UWN Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d Deposited 2017-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
104–274（171 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 8O7 N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonami de × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, 1.6 M ammonium sulfate
|
Resolution 3.20 Å R-free 0.234 |
| 6HV2 MMP-13 in complex with the peptide IMISF Deposited 2018-10-10 | 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
103–270（168 aa）
Chain B
163–167（5 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；50 mM glycine, 20% PEG4000, 1 M ammonium formate, pH 9.4
|
Resolution 1.71 Å R-free 0.263 |
| 7JU8 X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine Deposited 2020-08-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–274（171 aa）
Fragment：PROTEASE
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 9DY 4-(1,2,3-thiadiazol-4-yl)pyridine × 1 FMT FORMIC ACID × 6 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10% w/v PEG4000, 1 M ammonium formate, and 100 mM Tris, pH 8.0
|
Resolution 2.00 Å R-free 0.264 |
| 7JU8 X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine Deposited 2020-08-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–274（171 aa）
Fragment：PROTEASE
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 2 9DY 4-(1,2,3-thiadiazol-4-yl)pyridine × 1 FMT FORMIC ACID × 5 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10% w/v PEG4000, 1 M ammonium formate, and 100 mM Tris, pH 8.0
|
Resolution 2.00 Å R-free 0.264 |
| 830C COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID Deposited 1998-08-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
104–271（168 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 RS1 4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYLMETHYL]-TETRAHYDRO-PYRAN-4-CARBOXYLIC ACID HYDROXYAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；pH 8.0
|
Resolution 1.60 Å R-free 0.266 |
| 830C COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID Deposited 1998-08-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
104–271（168 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 RS1 4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYLMETHYL]-TETRAHYDRO-PYRAN-4-CARBOXYLIC ACID HYDROXYAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；pH 8.0
|
Resolution 1.60 Å R-free 0.266 |
48 other PDB entries and 105 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | MMP13_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–172； UniProt 103–274 Author chain B； PDBConstruct 1–172； UniProt 103–274 |
