SAXSdb — 3dpf

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

Neutrophil collagenase

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 100–262	Fragment：MMP-8 catalytic domain, UNP residues 100-262	CA CALCIUM ION × 2 ZN ZINC ION × 2 AXB N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide × 1 HAE ACETOHYDROXAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a reservoir buffer containing 1.0-2.0M sodium phosphate, 0.02% NaN3, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.270
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 100–262	Fragment：MMP-8 catalytic domain, UNP residues 100-262	CA CALCIUM ION × 2 ZN ZINC ION × 2 AXB N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a reservoir buffer containing 1.0-2.0M sodium phosphate, 0.02% NaN3, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.270

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 3DPF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A85 MMP8 WITH MALONIC AND ASPARAGINE BASED INHIBITOR Deposited 1998-04-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 105–262（158 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 0DY N~1~-(3-aminobenzyl)-N~2~-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-aspartamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1A86 MMP8 WITH MALONIC AND ASPARTIC ACID BASED INHIBITOR Deposited 1998-04-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 105–262（158 aa）	Not recorded	0ZB N-benzyl-N~2~-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-alpha-asparagine × 1 CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1BZS CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909 Deposited 1998-11-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 99–263（165 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 BSI 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PROTEIN SOLUTION: 10 MG/ML MMP8 IN 25 MM MES, 100 MM NACL, 20 MM CACL2, 0.1 MM ZNCL2, PH 6.0, WITH THREEFOLD EXCESS INHIBITOR IN DMF ADDED. RESERVOIR SOLUTION: 10-25% (W/W) PEG6000. CRYSTALS APPEAR IN ABOUT 1 WEEK., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å
1I73 COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) Deposited 2001-03-07	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 100–262（163 aa） Fragment：RESIDUES 80-242	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG 6000, MES-NaOH, NaCl, CaCl2, ZnCl2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.40 Å R-free 0.194
1I76 COMPLEX OF 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID (D-TIC DERIVATIVE) WITH T CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) Deposited 2001-03-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：RESIDUES 80-242	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 BSI 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG 6000, MES-NAOH, NaCl, CaCl2, ZnCl2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.20 Å R-free 0.171
1JAN COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (PHE79 FORM) Deposited 1996-03-11	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 99–262（164 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 79 - 242	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1JAO COMPLEX OF 3-MERCAPTO-2-BENZYLPROPANOYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) Deposited 1996-03-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 80 - 242	Not recorded	0D3 N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide × 1 CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1JAP COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) Deposited 1996-03-11	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 100–262（163 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 86 - 242	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.82 Å
1JAQ COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) Deposited 1996-03-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 80 - 242	Not recorded	CA CALCIUM ION × 2 01S N-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-alanylglycinamide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1JH1 Crystal Structure of MMP-8 complexed with a 6H-1,3,4-thiadiazine derived inhibitor Deposited 2001-06-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 105–262（158 aa） Fragment：MMP-8 catalytic domain	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 JST BUT-3-ENYL-[5-(4-CHLORO-PHENYL)-3,6-DIHYDRO-[1,3,4]THIADIAZIN-2-YLIDENE]-AMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1M MES, 10% PEG6K, 10mM CaCl2, 100mM NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.70 Å R-free 0.264
1JJ9 Crystal Structure of MMP8-Barbiturate Complex Reveals Mechanism for Collagen Substrate Recognition Deposited 2001-07-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：catalytic domain	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 BBT 2-HYDROXY-5-[4-(2-HYDROXY-ETHYL)-PIPERIDIN-1-YL]-5-PHENYL-1H-PYRIMIDINE-4,6-DIONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；PEG6000, 10mM CaCl2, 100mM NaCl, Cacodylate pH6.0, VAPOR DIFFUSION, temperature 291K	Resolution 2.00 Å R-free 0.296
1KBC PROCARBOXYPEPTIDASE TERNARY COMPLEX Deposited 1997-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 99–262（164 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 HLE 3-FORMYL-2-HYDROXY-5-METHYL-HEXANOIC ACID HYDROXYAMIDE × 1 RIN 3-AMINO-AZACYCLOTRIDECAN-2-ONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1KBC PROCARBOXYPEPTIDASE TERNARY COMPLEX Deposited 1997-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 99–262（164 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 HLE 3-FORMYL-2-HYDROXY-5-METHYL-HEXANOIC ACID HYDROXYAMIDE × 1 RIN 3-AMINO-AZACYCLOTRIDECAN-2-ONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1MMB COMPLEX OF BB94 WITH THE CATALYTIC DOMAIN OF MATRIX METALLOPROTEINASE-8 Deposited 1995-08-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 BAT 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1MNC STRUCTURE OF HUMAN NEUTROPHIL COLLAGENASE REVEALS LARGE S1' SPECIFICITY POCKET Deposited 1994-01-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 101–263（163 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 PLH METHYLAMINO-PHENYLALANYL-LEUCYL-HYDROXAMIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1ZP5 Crystal structure of the complex between MMP-8 and a N-hydroxyurea inhibitor Deposited 2005-05-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：Catalytic domain (80-242)	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 2NI N-{2-[(4'-CYANO-1,1'-BIPHENYL-4-YL)OXY]ETHYL}-N'-HYDROXY-N-METHYLUREA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG6000, MES/NAOH, Na Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.251
1ZS0 Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (S-enantiomer) Deposited 2005-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：Catalytic domain of neutrophil collagenase (Residues:80-242)	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 EIN (1S)-1-{[(4'-METHOXY-1,1'-BIPHENYL-4-YL)SULFONYL]AMINO}-2-METHYLPROPYLPHOSPHONIC ACID × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG6000, MES/NaOH, NaCl, CaCl2, ZnCl2, Na Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.56 Å R-free 0.235
1ZVX Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (R-enantiomer) Deposited 2005-06-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：catalytic domain of neutrophil collagenase (Residues:80-242)	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 FIN (1R)-1-{[(4'-METHOXY-1,1'-BIPHENYL-4-YL)SULFONYL]AMINO}-2-METHYLPROPYLPHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG6000, MES/NaOH, NaCl, CaCl2, ZnCl2, NaPhosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 1.87 Å R-free 0.244
2OY2 Human MMP-8 in complex with peptide IAG Deposited 2007-02-21	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 105–262（158 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.192
2OY2 Human MMP-8 in complex with peptide IAG Deposited 2007-02-21	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 F 105–262（158 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.192
2OY4 Uninhibited human MMP-8 Deposited 2007-02-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 105–262（158 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.70 Å R-free 0.293
2OY4 Uninhibited human MMP-8 Deposited 2007-02-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 105–262（158 aa） Fragment：CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.70 Å R-free 0.293
3DNG Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor Deposited 2008-07-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：MMP-8 catalytic domain, UNP residues 100-262	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 AXA (5S)-5-(2-amino-2-oxoethyl)-4-oxo-N-[(3-oxo-3,4-dihydro-2H-1,4-benzoxazin-6-yl)methyl]-3,4,5,6,7,8-hexahydro[1]benzothieno[2,3-d]pyrimidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a reservoir buffer containing 1.0-2.0M sodium phosphate, 0.02% NaN3, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.280
3DNG Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor Deposited 2008-07-02	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 100–262（163 aa） Fragment：MMP-8 catalytic domain, UNP residues 100-262	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 AXA (5S)-5-(2-amino-2-oxoethyl)-4-oxo-N-[(3-oxo-3,4-dihydro-2H-1,4-benzoxazin-6-yl)methyl]-3,4,5,6,7,8-hexahydro[1]benzothieno[2,3-d]pyrimidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a reservoir buffer containing 1.0-2.0M sodium phosphate, 0.02% NaN3, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.280
3DPE Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor Deposited 2008-07-08	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：MMP-8 catalytic domain, UNP residues 100-262	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 AXB N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a reservoir buffer containing 1.0-2.0M sodium phosphate, 0.02% NaN3, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.242
3TT4 Human MMP8 in complex with L-glutamate motif inhibitor Deposited 2011-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 104–262（159 aa） Fragment：MMP8 catalytic domain (UNP residues 104-262)	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 2 E1S N~2~-{3-[4-(5-methylthiophen-2-yl)phenyl]propanoyl}-L-alpha-glutamine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；MMP-8 at 400 micro-M co-crystallization with peptidic inhibitor with reservoir solution 17.5% PEG 20K, 0.1 M MES, 0.125 M NACL. VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K. Inhibitor exchange: 24hr soak in 25% PEG 4K instead of 17.5% PEG20K with 100 micro-M E1S inhibitor in 6 micro-L volume cryoprotectant is 12% PEG10K, 13.75% MPEG2K, 5% di-ethylene glycol, 10% 1,2-propanediol, 10% glycerol, 0.025 M MES PH 5.5, 30 sec cryoprotectant soak	Resolution 1.88 Å R-free 0.258
4QKZ X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115 Deposited 2014-06-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa） Fragment：catalytic domain, UNP residues 100-262	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 QZK {[(biphenyl-4-ylsulfonyl)amino]methanediyl}bis(phosphonic acid) × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10 % PEG 6000, 0.2M MES/NAOH, 1M NA PHOSPHATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.194
5H8X Crystal structure of the complex MMP-8/BF471 (catechol inhibitor) Deposited 2015-12-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–262（163 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 5XT ~{N}-[3,4-bis(oxidanyl)phenyl]-4-phenyl-benzenesulfonamide × 1 7FY ~{N}-[4,5-bis(oxidanylidene)cyclohexen-1-yl]-4-phenyl-benzenesulfonamide × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10 % PEG 6000, 0.2M MES/NAOH, 1M NA REMARK 280 PHOSPHATE, PH 6.0	Resolution 1.30 Å R-free 0.217

24 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MMP8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 100–262 Author chain B； PDBConstruct 1–163； UniProt 100–262

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3dpf
Deposition date deposition_date	2008-07-08
Structure title title	Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor
Keywords keywords	;hydrolase, selective inhibition, non-zinc chelating inhibitors, Calcium, Collagen degradation, Extracellular matrix, Glycoprotein, Metal-binding, Metalloprotease, Polymorphism, Protease, Secreted, Zinc, Zymogen ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.21 Å
Radius of gyration Rg (electron density) rg_electron	23.52 Å
Forward intensity I(0) i0	26229900.00
Molecular weight molecular_weight	37712.0 kDa
Excluded volume excluded_volume	46248 Å³
Envelope volume envelope_volume	55798 Å³
Hydration-shell volume shell_volume	20532 Å³
Envelope diameter envelope_diameter	78.3 Å
Shell Rg shell_rg	29.34 Å
Envelope Rg envelope_rg	23.33 Å
Shape Rg shape_rg	23.50 Å
Total Rg total_rg	24.25 Å
Total atoms total_atoms	2651
Residues n_residues	326
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.2 Å
Rg (real space) rg_real	24.30 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	2.6230e+07
I(0) uncertainty (real space) i0_real_error	3.4460e+05
Rg (reciprocal space) rg_reciprocal	24.28 Å
I(0) (reciprocal space) i0_reciprocal	26230000.0000
Solution quality estimate total_estimate	0.8881
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.372
Kurtosis Kurtosis kurtosis	-0.578
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5306000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Neutrophil collagenase
Molecular weight formula_weight	18111.7 kDa
EC 编号 ec_number	3.4.24.34
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3077

MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide ;
Molecular weight formula_weight	539.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ACETOHYDROXAMIC ACID
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	426

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3dpfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

Domain ID domain_id	d3dpfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	3dpfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	3dpfB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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8. Citations (4)

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Unit-cell length a length_a	68.300 Å
Unit-cell length b length_b	69.210 Å
Unit-cell length c length_c	81.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2380
R_free r_free	0.2700

fit	/app/data/saxs_computation/dp/3dpf/3dpf.fit
pddf	/app/data/pr_computation/dp/3dpf/3dpf.pr.out
profile	/app/data/saxs_computation/dp/3dpf/3dpf.dat

Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor