SAXSdb — 5h8x

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Neutrophil collagenase

Homo sapiens

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 100–262	未记录	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结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10 % PEG 6000, 0.2M MES/NAOH, 1M NA REMARK 280 PHOSPHATE, PH 6.0	分辨率 1.30 Å R-free 0.217

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 5H8X	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1A85 MMP8 WITH MALONIC AND ASPARAGINE BASED INHIBITOR 提交 1998-04-03	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 105–262（158 aa）	未记录	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 未提供已读取条件	分辨率 2.00 Å
1A86 MMP8 WITH MALONIC AND ASPARTIC ACID BASED INHIBITOR 提交 1998-04-03	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 105–262（158 aa）	未记录	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 未提供已读取条件	分辨率 2.00 Å
1BZS CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909 提交 1998-11-04	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 99–263（165 aa）片段：CATALYTIC DOMAIN	未记录	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结晶条件 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	分辨率 1.70 Å
1I73 COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) 提交 2001-03-07	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 100–262（163 aa）片段：RESIDUES 80-242	未记录	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG 6000, MES-NaOH, NaCl, CaCl2, ZnCl2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 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) 提交 2001-03-08	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：RESIDUES 80-242	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG 6000, MES-NAOH, NaCl, CaCl2, ZnCl2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 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) 提交 1996-03-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 99–262（164 aa）片段：CATALYTIC DOMAIN, RESIDUES 79 - 242	未记录	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.50 Å
1JAO COMPLEX OF 3-MERCAPTO-2-BENZYLPROPANOYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) 提交 1996-03-11	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：CATALYTIC DOMAIN, RESIDUES 80 - 242	未记录	0D3 N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide × 1 CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.40 Å
1JAP COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) 提交 1996-03-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 100–262（163 aa）片段：CATALYTIC DOMAIN, RESIDUES 86 - 242	未记录	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.82 Å
1JAQ COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) 提交 1996-03-11	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：CATALYTIC DOMAIN, RESIDUES 80 - 242	未记录	CA CALCIUM ION × 2 01S N-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-alanylglycinamide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.40 Å
1JH1 Crystal Structure of MMP-8 complexed with a 6H-1,3,4-thiadiazine derived inhibitor 提交 2001-06-27	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 105–262（158 aa）片段：MMP-8 catalytic domain	未记录	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结晶条件 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	分辨率 2.70 Å R-free 0.264
1JJ9 Crystal Structure of MMP8-Barbiturate Complex Reveals Mechanism for Collagen Substrate Recognition 提交 2001-07-04	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：catalytic domain	未记录	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结晶条件 VAPOR DIFFUSION；pH 6；291 K；PEG6000, 10mM CaCl2, 100mM NaCl, Cacodylate pH6.0, VAPOR DIFFUSION, temperature 291K	分辨率 2.00 Å R-free 0.296
1KBC PROCARBOXYPEPTIDASE TERNARY COMPLEX 提交 1997-04-29	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 99–262（164 aa）片段：CATALYTIC DOMAIN	未记录	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 未提供已读取条件	分辨率 1.80 Å
1KBC PROCARBOXYPEPTIDASE TERNARY COMPLEX 提交 1997-04-29	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 99–262（164 aa）片段：CATALYTIC DOMAIN	未记录	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 未提供已读取条件	分辨率 1.80 Å
1MMB COMPLEX OF BB94 WITH THE CATALYTIC DOMAIN OF MATRIX METALLOPROTEINASE-8 提交 1995-08-23	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：CATALYTIC DOMAIN	未记录	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 未提供已读取条件	分辨率 2.10 Å
1MNC STRUCTURE OF HUMAN NEUTROPHIL COLLAGENASE REVEALS LARGE S1' SPECIFICITY POCKET 提交 1994-01-12	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 101–263（163 aa）	未记录	ZN ZINC ION × 2 CA CALCIUM ION × 1 PLH METHYLAMINO-PHENYLALANYL-LEUCYL-HYDROXAMIC ACID × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.10 Å
1ZP5 Crystal structure of the complex between MMP-8 and a N-hydroxyurea inhibitor 提交 2005-05-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：Catalytic domain (80-242)	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG6000, MES/NAOH, Na Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.80 Å R-free 0.251
1ZS0 Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (S-enantiomer) 提交 2005-05-23	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：Catalytic domain of neutrophil collagenase (Residues:80-242)	未记录	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结晶条件 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	分辨率 1.56 Å R-free 0.235
1ZVX Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (R-enantiomer) 提交 2005-06-03	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：catalytic domain of neutrophil collagenase (Residues:80-242)	未记录	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结晶条件 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	分辨率 1.87 Å R-free 0.244
2OY2 Human MMP-8 in complex with peptide IAG 提交 2007-02-21	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 105–262（158 aa）片段：CATALYTIC DOMAIN	未记录	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.50 Å R-free 0.192
2OY2 Human MMP-8 in complex with peptide IAG 提交 2007-02-21	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 F 105–262（158 aa）片段：CATALYTIC DOMAIN	未记录	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.50 Å R-free 0.192
2OY4 Uninhibited human MMP-8 提交 2007-02-21	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 105–262（158 aa）片段：CATALYTIC DOMAIN	未记录	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.70 Å R-free 0.293
2OY4 Uninhibited human MMP-8 提交 2007-02-21	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 F 105–262（158 aa）片段：CATALYTIC DOMAIN	未记录	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 1.70 Å R-free 0.293
3DNG Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor 提交 2008-07-02	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：MMP-8 catalytic domain, UNP residues 100-262	未记录	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结晶条件 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	分辨率 2.00 Å R-free 0.280
3DNG Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor 提交 2008-07-02	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 100–262（163 aa）片段：MMP-8 catalytic domain, UNP residues 100-262	未记录	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结晶条件 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	分辨率 2.00 Å R-free 0.280
3DPE Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor 提交 2008-07-08	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：MMP-8 catalytic domain, UNP residues 100-262	未记录	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结晶条件 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	分辨率 1.60 Å R-free 0.242
3DPF Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor 提交 2008-07-08	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：MMP-8 catalytic domain, UNP residues 100-262	未记录	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结晶条件 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	分辨率 2.10 Å R-free 0.270
3DPF Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor 提交 2008-07-08	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 100–262（163 aa）片段：MMP-8 catalytic domain, UNP residues 100-262	未记录	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结晶条件 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	分辨率 2.10 Å R-free 0.270
3TT4 Human MMP8 in complex with L-glutamate motif inhibitor 提交 2011-09-14	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 104–262（159 aa）片段：MMP8 catalytic domain (UNP residues 104-262)	未记录	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结晶条件 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	分辨率 1.88 Å R-free 0.258
4QKZ X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115 提交 2014-06-10	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 100–262（163 aa）片段：catalytic domain, UNP residues 100-262	未记录	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结晶条件 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	分辨率 1.20 Å R-free 0.194

共 24 个其他 PDB 条目、29 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	MMP8_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–163； UniProt 100–262

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	5h8x
沉积日期 deposition_date	2015-12-24
结构标题 title	Crystal structure of the complex MMP-8/BF471 (catechol inhibitor)
关键词 keywords	Catechol function, MMPs, inhibitor, metalloprotese, zinc binding function, hydrolase; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	15.88 Å
回转半径 Rg (电子) rg_electron	14.54 Å
零角强度 I(0) i0	7161790.00
分子量 molecular_weight	18832.0 kDa
排除体积 excluded_volume	23146 Å³
包络体积 envelope_volume	25282 Å³
水化壳体积 shell_volume	14320 Å³
包络直径 envelope_diameter	45.6 Å
壳层 Rg shell_rg	20.84 Å
包络 Rg envelope_rg	14.87 Å
形状 Rg shape_rg	14.51 Å
总 Rg total_rg	15.73 Å
总原子数 total_atoms	1323
残基数 n_residues	163
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	47.6 Å
Rg (实空间) rg_real	15.74 Å
Rg 误差 (实空间) rg_real_error	0.20 Å
I(0) (实空间) i0_real	7.1620e+06
I(0) 误差 (实空间) i0_real_error	7.7790e+04
Rg (倒空间) rg_reciprocal	15.75 Å
I(0) (倒空间) i0_reciprocal	7162000.0000
解质量估计 total_estimate	0.9003
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	21.1 Å
偏度 Skewness skewness	0.039
峰度 Kurtosis kurtosis	-0.455
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1518000.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.980

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (7)

实体 1 Entity 1 polymer

描述 description	Neutrophil collagenase
分子量 formula_weight	18111.7 kDa
EC 编号 ec_number	3.4.24.34
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	1508

MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG

来源 Source

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

实体 2 Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 3 Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 4 Entity 4 non-polymer

描述 description	~{N}-[3,4-bis(oxidanyl)phenyl]-4-phenyl-benzenesulfonamide
分子量 formula_weight	341.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 5 Entity 5 non-polymer

描述 description	~{N}-[4,5-bis(oxidanylidene)cyclohexen-1-yl]-4-phenyl-benzenesulfonamide
分子量 formula_weight	341.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 6 Entity 6 non-polymer

描述 description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
分子量 formula_weight	195.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 7 Entity 7 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	161

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7. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d5h8xa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (1 domains)

结构域编号 domain_id	5h8xA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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8. 引用文献 (1)

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晶胞边长 a length_a	32.910 Å
晶胞边长 b length_b	68.460 Å
晶胞边长 c length_c	68.530 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.300 Å
最低分辨率 resolution_low	29.666 Å
R 因子 r_factor	0.1962
R_work r_work	0.1951
R_free r_free	0.2172

fit	/app/data/saxs_computation/h8/5h8x/5h8x.fit
pddf	/app/data/pr_computation/h8/5h8x/5h8x.pr.out
profile	/app/data/saxs_computation/h8/5h8x/5h8x.dat

Crystal structure of the complex MMP-8/BF471 (catechol inhibitor)