SAXSdb — 1bzs

▼

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 99–263	Fragment：CATALYTIC DOMAIN	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

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 1BZS	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
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 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：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 construct Different ligand/ion Different experimental conditions 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 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：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
3DPF Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor Deposited 2008-07-08	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：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 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
3DPF Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor Deposited 2008-07-08	Different construct Different ligand/ion Different experimental conditions 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 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
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 29 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 1–165； UniProt 99–263

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bzs
Deposition date deposition_date	1998-11-04
Structure title title	CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909
Keywords keywords	METALLO PROTEINASE, HYDROXAMATE, MATRIX DEGRADATION, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.10 Å
Radius of gyration Rg (electron density) rg_electron	14.66 Å
Forward intensity I(0) i0	7362680.00
Molecular weight molecular_weight	19189.0 kDa
Excluded volume excluded_volume	23615 Å³
Envelope volume envelope_volume	25789 Å³
Hydration-shell volume shell_volume	14499 Å³
Envelope diameter envelope_diameter	50.0 Å
Shell Rg shell_rg	20.99 Å
Envelope Rg envelope_rg	14.97 Å
Shape Rg shape_rg	14.64 Å
Total Rg total_rg	15.84 Å
Total atoms total_atoms	1349
Residues n_residues	165
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

▼

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

Maximum dimension Dmax dmax	51.2 Å
Rg (real space) rg_real	15.96 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	7.3630e+06
I(0) uncertainty (real space) i0_real_error	8.1270e+04
Rg (reciprocal space) rg_reciprocal	15.98 Å
I(0) (reciprocal space) i0_reciprocal	7363000.0000
Solution quality estimate total_estimate	0.8842
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.054
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1538000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.978

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	NEUTROPHIL COLLAGENASE
Molecular weight formula_weight	18374.0 kDa
EC 编号 ec_number	3.4.24.34
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1557

FMLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYGD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

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	2

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	2

Entity 4 Entity 4 non-polymer

Description description	2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID
Molecular weight formula_weight	393.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 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	208

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bzsa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id	1bzsA00
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)

▶

8. Citations (1)

▶

Unit-cell length a length_a	33.100 Å
Unit-cell length b length_b	68.900 Å
Unit-cell length c length_c	70.500 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	4

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	—

fit	/app/data/saxs_computation/bz/1bzs/1bzs.fit
pddf	/app/data/pr_computation/bz/1bzs/1bzs.pr.out
profile	/app/data/saxs_computation/bz/1bzs/1bzs.dat

CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909