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5om6

Crystal structure of Alpha1-antichymotrypsin variant DBS-I-allo2: a MMP9-cleavable drug-binding serpin for doxycycline

Method: X-RAY DIFFRACTION Dmax: 110.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-1-antichymotrypsin

Homo sapiens

UniProt P01011

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 26–383 Chain B； UniProt 384–423 Fragment：UNP residues 36-383 Mutation：L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L I357G T358P L359R L360Q Fragment：UNP residues 384-423 Mutation：L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L I357G T358P L359R L360Q CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M citric acid pH 3.5, 25 % w/v PEG 3350 Resolution 1.85 Å R-free 0.238
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 26–383 Chain D； UniProt 384–423 Fragment：UNP residues 36-383 Mutation：L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L I357G T358P L359R L360Q Fragment：UNP residues 384-423 Mutation：L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L I357G T358P L359R L360Q CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M citric acid pH 3.5, 25 % w/v PEG 3350 Resolution 1.85 Å R-free 0.238

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 5OM6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AS4 CLEAVED ANTICHYMOTRYPSIN A349R Deposited 1997-08-12 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 43–383（341 aa） Fragment：CHAIN A CONTAINS RESIDUES 20 - 358, CHAIN B CONTAINS RESIDUES 359 - 393
Chain B 387–423（37 aa） Fragment：CHAIN A CONTAINS RESIDUES 20 - 358, CHAIN B CONTAINS RESIDUES 359 - 393
Mutation：A349R Mutation：A349R ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；14% PEG MONOMETHYLETHER 5000, 0.2 M MAGNESIUM ACETATE 0.1 M SODIUM ACETATE PH 5.6 PROTEIN AT 3 MG/ML
Resolution 2.10 Å R-free 0.240
1QMN Alpha1-antichymotrypsin serpin in the delta conformation (partial loop insertion) Deposited 1999-10-04 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 26–423（398 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；1 MICROLITER OF 10MG/ML PROTEIN IN 50MM TRIS, 50MM KCL, PH 7.4 WAS MIXED WITH 2 MICROLITER OF PRECIPITANT AND EQUILIBRATED AS A HANGING DROP OVER 1ML OF PRECIPITANT (20% [W/V] PEG 4000, 0.2M AMMONIUM SULPHATE, 0.1M NAOAC, PH 4.5), AT 18 DEGREES C
Resolution 2.27 Å R-free 0.243
2ACH CRYSTAL STRUCTURE OF CLEAVED HUMAN ALPHA1-ANTICHYMOTRYPSIN AT 2.7 ANGSTROMS RESOLUTION AND ITS COMPARISON WITH OTHER SERPINS Deposited 1993-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–383（360 aa）
Chain B 384–423（40 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
2ACH CRYSTAL STRUCTURE OF CLEAVED HUMAN ALPHA1-ANTICHYMOTRYPSIN AT 2.7 ANGSTROMS RESOLUTION AND ITS COMPARISON WITH OTHER SERPINS Deposited 1993-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 24–383（360 aa）
Chain B 384–423（40 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
3CAA CLEAVED ANTICHYMOTRYPSIN A347R Deposited 1997-08-18 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 43–383（341 aa）
Chain B 387–423（37 aa）
Mutation：A347R Mutation：A347R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；10% PEG MONOMETHYLETHER 5000 0.2 M MAGNESIUM ACETATE 0.1 M SODIUM CITRATE PH 5.6 PROTEIN AT 3 MG/ML
Resolution 2.40 Å R-free 0.280
3DLW Antichymotrypsin Deposited 2008-06-29 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 25–423（399 aa）
Mutation：A351G, A352T, V370T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG 10,000, HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.70 Å R-free 0.286
4CAA CLEAVED ANTICHYMOTRYPSIN T345R Deposited 1997-08-14 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 43–383（341 aa）
Chain B 387–423（37 aa）
Mutation：T345R Mutation：T345R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；14% PEG 8000 0.2 M MAGNESIUM ACETATE 0.1 M SODIUM CITRATE PH 5.6
Resolution 2.90 Å R-free 0.284
5OM2 Crystal structure of Alpha1-antichymotrypsin variant DBS-I1: a drug-binding serpin for doxycycline Deposited 2017-07-28 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274A W276F R277F V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383H D384F Q386W N387S ; Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274A W276F R277F V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383H D384F Q386W N387S ; EDO 1,2-ETHANEDIOL × 1 DXT (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium chloride, 20 % w/v PEG 3350
Resolution 1.47 Å R-free 0.202
5OM3 Crystal structure of Alpha1-antichymotrypsin variant DBS-I5: a MMP14-cleavable drug-binding serpin for doxycycline Deposited 2017-07-28 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F V355L K356F T358P L360S S361L A362R L363M P382D T383H D384F Q386W N387S Mutation：L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F V355L K356F T358P L360S S361L A362R L363M P382D T383H D384F Q386W N387S PEG DI(HYDROXYETHYL)ETHER × 1 DXT (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v PEG 3350
Resolution 2.00 Å R-free 0.219
5OM5 Crystal structure of Alpha1-antichymotrypsin variant DBS-I-allo1: an allosterically triggered drug-binding serpin for doxycycline Deposited 2017-07-28 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383H D384F Q386W N387S ; Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383H D384F Q386W N387S ; EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.0, 30 % v/v Jeffamine ED-2001 pH 7.0
Resolution 1.59 Å R-free 0.196
5OM7 Crystal structure of Alpha1-antichymotrypsin variant DBS-II: a drug-binding serpin for doxorubicin Deposited 2017-07-28 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S ; Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S ; DM2 DOXORUBICIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium chloride, 20 % w/v PEG 3350
Resolution 1.73 Å R-free 0.235
5OM8 Crystal form 2 of Alpha1-antichymotrypsin variant DBS-II-allo: an allosterically modulated drug-binding serpin for doxorubicin Deposited 2017-07-28 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E A349R V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S ; Mutation：;L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E A349R V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S ; CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium chloride, 20% w/v PEG 3350
Resolution 2.20 Å R-free 0.242
6FTP Crystal form 1 of Alpha1-antichymotrypsin variant DBS-II-allo: an allosterically modulated drug-binding serpin for doxorubicin Deposited 2018-02-22 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 26–383（358 aa）
Chain B 386–423（38 aa）
Mutation：L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E A349R V355L K356E I357V T358L L359F L360Q Mutation：S361G A362P P382D T383N D384F Q386W N387S EDO 1,2-ETHANEDIOL × 3 DM2 DOXORUBICIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium thiocyanate, 20 % w/v PEG 3350
Resolution 1.80 Å R-free 0.221
6HGD Crystal structure of Alpha1-antichymotrypsin variant NewBG-0: a new binding globulin variant that is devoid of any cortisol-binding capabilities Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, E242Q, K244N, K274N, R277G Mutation：P382D, T383H, D384F, Q386W No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-Tris pH 6.5, 25 % w/v PEG 3350
Resolution 1.90 Å R-free 0.198
6HGE Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in the uncleaved S-conformation Deposited 2018-08-23 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 26–423（398 aa）
Mutation：L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, D384F, Q386W, N387S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, adenosine 3,5-cyclic monophosphate sodium salt monohydrate, sarcosine, 4-aminobenzoic acid, acarbose, inosine, 0.02 M HEPES sodium pH 6.8
Resolution 2.80 Å R-free 0.262
6HGE Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in the uncleaved S-conformation Deposited 2018-08-23 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 26–423（398 aa）
Mutation：L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, D384F, Q386W, N387S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, adenosine 3,5-cyclic monophosphate sodium salt monohydrate, sarcosine, 4-aminobenzoic acid, acarbose, inosine, 0.02 M HEPES sodium pH 6.8
Resolution 2.80 Å R-free 0.262
6HGE Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in the uncleaved S-conformation Deposited 2018-08-23 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 26–423（398 aa）
Mutation：L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, D384F, Q386W, N387S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, adenosine 3,5-cyclic monophosphate sodium salt monohydrate, sarcosine, 4-aminobenzoic acid, acarbose, inosine, 0.02 M HEPES sodium pH 6.8
Resolution 2.80 Å R-free 0.262
6HGE Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in the uncleaved S-conformation Deposited 2018-08-23 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 26–423（398 aa）
Mutation：L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, D384F, Q386W, N387S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, adenosine 3,5-cyclic monophosphate sodium salt monohydrate, sarcosine, 4-aminobenzoic acid, acarbose, inosine, 0.02 M HEPES sodium pH 6.8
Resolution 2.80 Å R-free 0.262
6HGF Crystal structure of Alpha1-antichymotrypsin variant NewBG-II: a new binding globulin in complex with cortisol Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, E242Q, K244N, L269S, P270R, K274A, R277G Mutation：P382D, T383H, D384F, Q386W, N387S EDO 1,2-ETHANEDIOL × 2 HCY (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate, 20 % w/v PEG 3350
Resolution 1.65 Å R-free 0.187
6HGG Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with cortisol Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G Mutation：P382D, T383H, D384F, Q386W, N387S HCY (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 % v/v Tacsimate pH 5.0, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 16 % w/v PEG 3350
Resolution 1.79 Å R-free 0.216
6HGH Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin without any bound ligand Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G Mutation：P382D, T383H, D384F, Q386W, N387S MLA MALONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；4 % Tacsimate pH 4.0, 12 % w/v PEG 3350
Resolution 1.90 Å R-free 0.240
6HGI Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with corticosterone Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G Mutation：P382D, T383H, D384F, Q386W, N387S C0R CORTICOSTERONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 % v/v Tacsimate pH 5.0, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 16 % w/v PEG 3350
Resolution 1.52 Å R-free 0.193
6HGJ Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with aldosterone Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G Mutation：P382D, T383H, D384F, Q386W, N387S AS4 ALDOSTERONE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；2 % v/v Tacsimate pH 5.0, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 16 % w/v PEG 3350
Resolution 1.82 Å R-free 0.221
6HGK Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with progesterone Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G Mutation：P382D, T383H, D384F, Q386W, N387S STR PROGESTERONE × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 % Tacsimate pH 6.0, 0.1 M BIS-Tris pH 6.5, 20 % w/v PEG 3350
Resolution 1.85 Å R-free 0.227
6HGL Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with testosterone Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G Mutation：P382D, T383H, D384F, Q386W, N387S TES TESTOSTERONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2 % v/v Tacsimate pH 5.0, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 16 % w/v PEG 3350
Resolution 1.92 Å R-free 0.224
6HGM Crystal structure of Alpha1-antichymotrypsin variant NewBG-III-allo: an allosterically controlled new binding globulin with an unprecedentedly high ligand release efficacy Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G, A349R Mutation：P382D, T383H, D384F, Q386W, N387S CL CHLORIDE ION × 3 CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride dihydrate, 20 % w/v PEG 3350
Resolution 1.37 Å R-free 0.181
6HGN Crystal structure of Alpha1-antichymotrypsin variant DBS-II-allo-L55V: an allosterically controlled doxorubicin-binding serpin with an unprecedentedly high ligand release efficacy Deposited 2018-08-23 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 26–383（358 aa）
Chain B 384–423（40 aa）
Mutation：L24R, L55V, W194F,W215Y, E242Q, K244N, L269S, P270Q, K274S, W276F, R277F, D278E, A349R, V355L, K356E, I357V, T358L, L359F, L360Q Mutation：S361G, A362P, P382D, T383N, D384F, Q386W, N387S EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2 % Tacsimate pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16 % w/v PEG 3,350
Resolution 1.48 Å R-free 0.199
9C2T Infectious B19V capsid Deposited 2024-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain S 48–422（375 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9D7K Infectious B19V capsid Deposited 2024-08-16 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 S 1–423（423 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

25 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AACT_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 12–369； UniProt 26–383 Author chain C； PDBConstruct 12–369； UniProt 26–383 Author chain B； PDBConstruct 1–40； UniProt 384–423 Author chain D； PDBConstruct 1–40； UniProt 384–423

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5om6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5om6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5om6
Deposition date deposition_date2017-07-28
Structure title titleCrystal structure of Alpha1-antichymotrypsin variant DBS-I-allo2: a MMP9-cleavable drug-binding serpin for doxycycline
Keywords keywordsSerpin, alpha1-Antichymotrypsin, Doxycycline-binding protein, MMP9-cleavable RCL, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.49 Å
Radius of gyration Rg (electron density) rg_electron33.58 Å
Forward intensity I(0) i0108636000.00
Molecular weight molecular_weight85887.0 kDa
Excluded volume excluded_volume108510 ų
Envelope volume envelope_volume139950 ų
Hydration-shell volume shell_volume34619 ų
Envelope diameter envelope_diameter110.6 Å
Shell Rg shell_rg40.50 Å
Envelope Rg envelope_rg33.09 Å
Shape Rg shape_rg33.59 Å
Total Rg total_rg34.09 Å
Total atoms total_atoms6047
Residues n_residues752
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.2 Å
Rg (real space) rg_real34.54 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real1.0860e+08
I(0) uncertainty (real space) i0_real_error1.7650e+06
Rg (reciprocal space) rg_reciprocal34.52 Å
I(0) (reciprocal space) i0_reciprocal108600000.0000
Solution quality estimate total_estimate0.8806
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.8 Å
Skewness Skewness skewness0.248
Kurtosis Kurtosis kurtosis-0.790
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha71700000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.912
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5om6A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily10 — Antithrombin, subunit I, domain 2
Domain ID domain_id5om6A02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
Domain ID domain_id5om6C01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily10 — Antithrombin, subunit I, domain 2
Domain ID domain_id5om6C02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
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8. Citations (1)

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9. Files and Curves (10)