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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 104–471 Chain W； UniProt 25–50 | Fragment：Inactive full form (UNP residues 104-471) Mutation：E223A Fragment：pro-domain fragment (UNP residues 25-50) | 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 |
| 2 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain B； UniProt 104–471 Chain X； UniProt 25–50 | Fragment：Inactive full form (UNP residues 104-471) Mutation：E223A Fragment：pro-domain fragment (UNP residues 25-50) | 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 |
| 3 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain C； UniProt 104–471 Chain Y； UniProt 25–50 | Fragment：Inactive full form (UNP residues 104-471) Mutation：E223A Fragment：pro-domain fragment (UNP residues 25-50) | 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 |
| 4 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain D； UniProt 104–471 Chain Z； UniProt 25–50 | Fragment：Inactive full form (UNP residues 104-471) Mutation：E223A Fragment：pro-domain fragment (UNP residues 25-50) | 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 |
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 4G0D | 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
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 mutation/modification Different oligomeric state 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
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 mutation/modification Different oligomeric state 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 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 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 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 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 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 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 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 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 |
| 4JP4 Mmp13 in complex with a reverse hydroxamate Zn-binder Deposited 2013-03-19 | Different construct Different mutation/modification 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 construct Different mutation/modification Different oligomeric state 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 |
| 5B5P Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
103–274（172 aa）
Fragment：catalytic domain, residues 103-274
|
Not recorded | 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 |
| 5B5P Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state 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 × 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 |
| 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 mutation/modification Different oligomeric state 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 103 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | MMP13_HUMAN |
| Isoform | — |
| PDB entities | 1, 2 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–368； UniProt 104–471 Author chain B； PDBConstruct 1–368； UniProt 104–471 Author chain C； PDBConstruct 1–368； UniProt 104–471 Author chain D； PDBConstruct 1–368； UniProt 104–471 Author chain W； PDBConstruct 1–26； UniProt 25–50 Author chain X； PDBConstruct 1–26； UniProt 25–50 Author chain Y； PDBConstruct 1–26； UniProt 25–50 Author chain Z； PDBConstruct 1–26； UniProt 25–50 |
