2gkr

Crystal structure of the N-terminally truncated OMTKY3-del(1-5)

Method: X-RAY DIFFRACTION D_max: 36.9 Å Quality: REASONABLE

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

Ovomucoid

Meleagris gallopavo

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 I； UniProt 135–185	Fragment：turkey ovomucoid third domain, del (1-5)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES-Na pH 7.5, 10% v/v isopropanol, 20% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.16 Å R-free 0.177

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 2GKR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CHO CRYSTAL AND MOLECULAR STRUCTURES OF THE COMPLEX OF ALPHA-*CHYMOTRYPSIN WITH ITS INHIBITOR TURKEY OVOMUCOID THIRD DOMAIN AT 1.8 ANGSTROMS RESOLUTION Deposited 1988-03-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 130–185（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1CSO CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-ILE18I IN COMPLEX WITH SGPB Deposited 1999-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN ILE18-OMTKY3	Mutation：DEL 1-5, L18I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 4000 sodium potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å
1CT0 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-SER18I IN COMPLEX WITH SGPB Deposited 1999-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN SER18-OMTKY3	Mutation：DEL 1-5, L18S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 4000 sodium potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å
1CT2 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-THR18I IN COMPLEX WITH SGPB Deposited 1999-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN OMTKY3-THR18I	Mutation：DEL 1-5, L18T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 4000 sodium potassium phosphate , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å
1CT4 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-VAL18I IN COMPLEX WITH SGPB Deposited 1999-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN OMTKY3-VAL18I	Mutation：DEL 1-5, L18V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000 sodium potassium phosphate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å
1DS2 CRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I Deposited 2000-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN (OMTKY3)	Mutation：ESTER BOND BETWEEN THR17I-LEU18I(1LU) 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, HANGING DROP；pH 7.1；298 K；PEG 4000, sodium potassium phosphate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å
1DS3 CRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I Deposited 2000-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN (OMTKY3)	Mutation：REDUCED PEPTIDE BOND BETWEEN LEU18I(2LU)-ASP19I 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, HANGING DROP；298 K；ammonium sulphate, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.65 Å R-free 0.230
1HJA LYS 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH ALPHA-CHYMOTRYPSIN Deposited 1997-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN, DELETION OF FIRST 5 RESIDUES FROM N-TERMINUS	Mutation：DEL(1-5), L18K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M KH2PO4/K2HPO4 PH=6.0 10% PEG6000	Resolution 2.30 Å R-free 0.246
1OMT SOLUTION STRUCTURE OF OVOMUCOID (THIRD DOMAIN) FROM DOMESTIC TURKEY (298K, PH 4.1) (NMR, 50 STRUCTURES) (STANDARD NOESY ANALYSIS) Deposited 1995-10-11	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 130–185（56 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1OMU SOLUTION STRUCTURE OF OVOMUCOID (THIRD DOMAIN) FROM DOMESTIC TURKEY (298K, PH 4.1) (NMR, 50 STRUCTURES) (REFINED MODEL USING NETWORK EDITING ANALYSIS) Deposited 1995-10-11	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 130–185（56 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1R0R 1.1 Angstrom Resolution Structure of the Complex Between the Protein Inhibitor, OMTKY3, and the Serine Protease, Subtilisin Carlsberg Deposited 2003-09-22	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 I 135–185（51 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M ammonium dihydrogen phosphate, 0.1 M Tris, and 50%(v/v) 2-methyl-2,4-pentanediol (MPD), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.10 Å R-free 0.184
1SGD ASP 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18D	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.4M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 6.5	Resolution 1.80 Å
1SGE GLU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18E	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 6.5	Resolution 1.80 Å
1SGN ASN 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18N	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；2% PEG 6000, 50MM SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 6.5, pH 6.50	Resolution 1.80 Å
1SGP ALA 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1995-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa）	Mutation：DEL(1-6), L18A	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å
1SGQ GLY 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1995-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa）	Mutation：DEL(1-6), L18G	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1SGR LEU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1995-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa）	Mutation：DEL(1-6)	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1SGY TYR 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18Y	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 6.5	Resolution 1.80 Å
1TUR SOLUTION STRUCTURE OF TURKEY OVOMUCOID THIRD DOMAIN AS DETERMINED FROM NUCLEAR MAGNETIC RESONANCE DATA Deposited 1994-07-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 130–185（56 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1TUS SOLUTION STRUCTURE OF REACTIVE-SITE HYDROLYZED TURKEY OVOMUCOID THIRD DOMAIN BY NUCLEAR MAGNETIC RESONANCE AND DISTANCE GEOMETRY METHODS Deposited 1994-07-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 130–185（56 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1YU6 Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex Deposited 2005-02-11	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 C 1–185（185 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；10% ethylene glycol, 480 mM sodium malate, 75 mM sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.205
1YU6 Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex Deposited 2005-02-11	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 D 1–185（185 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；10% ethylene glycol, 480 mM sodium malate, 75 mM sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.205
1Z7K Crystal Structure of Trypsin- Ovomucoid turkey egg white inhibitor complex Deposited 2005-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 65–126（62 aa） Fragment：Second domain, residues 2-63 Chain C 12–15（4 aa） Fragment：First domain, residues 1-4	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1.5M ammonium sulphate, 10mM zinc acetate, 50mM Acetate buffer, pH 5.30, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.188
2GKT Crystal structure of the P14'-Ala32 variant of the N-terminally truncated OMTKY3-del(1-5) Deposited 2006-04-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 135–185（51 aa） Fragment：turkey ovomucoid third domain del (1-5)	Mutation：G32A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES-Na pH 7.5, 10% v/v isopropanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.23 Å R-free 0.151
2GKV Crystal structure of the SGPB:P14'-Ala32 OMTKY3-del(1-5) complex Deposited 2006-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 135–185（51 aa） Fragment：turkey ovomucoid third domain	Mutation：G32A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2M Na acetate trihydrate, 0.1M Tris-HCl pH 8.5, 26% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.248
2GKV Crystal structure of the SGPB:P14'-Ala32 OMTKY3-del(1-5) complex Deposited 2006-04-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 135–185（51 aa） Fragment：turkey ovomucoid third domain	Mutation：G32A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2M Na acetate trihydrate, 0.1M Tris-HCl pH 8.5, 26% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.248
2NU0 Molecular structures of the complexes of SGPB with OMTKY3 aromatic P1 variants Trp18I, His18I, Phe18I, and Tyr18I Deposited 2006-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：third domain, residues 135-185	Mutation：L18W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å
2NU1 Molecular structures of the complexes of SGPB with OMTKY3 aromatic P1 variants Trp18I, His18I, Phe18I and Tyr18I Deposited 2006-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：third domain, residues 135-185	Mutation：L18H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å
2NU2 Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I Deposited 2006-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：third domain, residues 135-185	Mutation：L18R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å
2NU3 Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I Deposited 2006-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：third domain, residues 135-185	Mutation：L18K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å
2NU4 Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I Deposited 2006-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：third domain, residues 135-185	Mutation：L18K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE at pH 7.1 24h before data collection, crystal was transferred to PEG4000, NaKHPO4 at pH 10.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å
2SGD ASP 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 10.7 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18D	PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.7；0.4M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 10.7	Resolution 1.80 Å
2SGE GLU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 10.7 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18E	PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.7；0.4M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 10.7	Resolution 1.80 Å
2SGF PHE 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18F	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE AT PH 6.5	Resolution 1.75 Å
2SGP PRO 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18P	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 6.5, pH 6.50	Resolution 1.80 Å
2SGQ GLN 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-6), L18Q	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 6.5	Resolution 1.80 Å
3SGB STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT 1.8 ANGSTROMS RESOLUTION Deposited 1983-01-21	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 I 130–185（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
3SGQ GLN 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 10.7 Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 135–185（51 aa） Fragment：THIRD DOMAIN	Mutation：DEL(1-5), L18Q	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.7；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 10.7	Resolution 1.80 Å

36 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IOVO_MELGA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain I； PDBConstruct 1–51； UniProt 135–185

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2gkr
Deposition date deposition_date	2006-04-03
Structure title title	Crystal structure of the N-terminally truncated OMTKY3-del(1-5)
Keywords keywords	reactive-site loop, alpha-helix, antiparallel beta-sheet, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
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	11.43 Å
Radius of gyration Rg (electron density) rg_electron	10.14 Å
Forward intensity I(0) i0	869471.00
Molecular weight molecular_weight	5615.0 kDa
Excluded volume excluded_volume	6820 Å³
Envelope volume envelope_volume	7546 Å³
Hydration-shell volume shell_volume	6716 Å³
Envelope diameter envelope_diameter	35.4 Å
Shell Rg shell_rg	15.05 Å
Envelope Rg envelope_rg	10.48 Å
Shape Rg shape_rg	10.10 Å
Total Rg total_rg	11.60 Å
Total atoms total_atoms	388
Residues n_residues	51
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	36.9 Å
Rg (real space) rg_real	11.38 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	8.6950e+05
I(0) uncertainty (real space) i0_real_error	7.4140e+03
Rg (reciprocal space) rg_reciprocal	11.38 Å
I(0) (reciprocal space) i0_reciprocal	869500.0000
Solution quality estimate total_estimate	0.7216
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.9 Å
Skewness Skewness skewness	0.156
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	74250.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 1.000; Smooth: 0.942

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ovomucoid
Molecular weight formula_weight	5585.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I
Atom count atom_count	456

VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC

来源 Source

来源生物 organism	Meleagris gallopavo
通用名 common_name	turkey
NCBI Class编号 ncbi_taxonomy_id	9103
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2gkri_
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.1 — Ovomucoid domain III-like

CATH v4.4 (1 domains)

Domain ID domain_id	2gkrI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	22.900 Å
Unit-cell length b length_b	34.429 Å
Unit-cell length c length_c	25.794 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.160 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1503
R_work r_work	0.1472
R_free r_free	0.1773

fit	/app/data/saxs_computation/gk/2gkr/2gkr.fit
pddf	/app/data/pr_computation/gk/2gkr/2gkr.pr.out
profile	/app/data/saxs_computation/gk/2gkr/2gkr.dat