3otp

Crystal structure of the DegP dodecamer with a model substrate

Method: X-RAY DIFFRACTION D_max: 155.7 Å Quality: GOOD

▼

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

Protease do

Escherichia coli

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 heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 27–474 Chain B； UniProt 27–474 Chain C； UniProt 27–474 Chain D； UniProt 27–474 Chain E； UniProt 27–474 Chain F； UniProt 27–474	Fragment：UNP residues 27-474 Mutation：S210A	Lysozyme C × 12 （B8YK79）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.6；291 K；65 mM citric acid, 35 mM Bis-Tris propane, 8% PEG3350, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K	Resolution 3.76 Å R-free 0.251

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 3OTP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KY9 Crystal Structure of DegP (HtrA) Deposited 2002-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 27–474（448 aa）	Mutation：S210A 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；pH 8.5；291 K；Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.80 Å R-free 0.275
1KY9 Crystal Structure of DegP (HtrA) Deposited 2002-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain B 27–474（448 aa）	Mutation：S210A 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；pH 8.5；291 K；Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.80 Å R-free 0.275
2ZLE Cryo-EM structure of DegP12/OMP Deposited 2008-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 27–474（448 aa） Chain B 27–474（448 aa） Chain C 27–474（448 aa） Chain E 27–474（448 aa） Chain F 27–474（448 aa） Chain G 27–474（448 aa） Chain H 27–474（448 aa） Chain I 27–474（448 aa） Chain J 27–474（448 aa） Chain K 27–474（448 aa） Chain L 27–474（448 aa） Chain M 27–474（448 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；Embedded in vitreous ice using C-flat holey carbon grids (CF-2/2-4C-100, Protochip) and a Vitrobot (FEI) at 20 temperature and 100% relative humidity	Resolution 28.00 Å
3CS0 Crystal structure of DegP24 Deposited 2008-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain A 27–474（448 aa）	Mutation：S210A 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；pH 8.5；292 K；PEG 550 MME, NaCl, pH 8.5, vapor diffusion, temperature 292K	Resolution 3.00 Å R-free 0.274
3MH4 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 27–474（448 aa）	Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.10 Å R-free 0.309
3MH4 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain B 27–474（448 aa）	Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.10 Å R-free 0.309
3MH5 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 27–474（448 aa）	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.00 Å R-free 0.309
3MH5 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain B 27–474（448 aa）	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.00 Å R-free 0.309
3MH6 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 27–474（448 aa）	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.60 Å R-free 0.309
3MH7 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain A 27–474（448 aa）	Mutation：S210A 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；pH 8.5；292 K；PEG 550 MME, NaCl, pH 8.5, VAPOR DIFFUSION, temperature 292K	Resolution 2.96 Å R-free 0.249
3OU0 re-refined 3CS0 Deposited 2010-09-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 27–474（448 aa） Fragment：DegP, UNP residues 27-474	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.229
4A8D DegP dodecamer with bound OMP Deposited 2011-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 27–474（448 aa） Fragment：DEGP Chain B 27–474（448 aa） Fragment：DEGP Chain C 27–474（448 aa） Fragment：DEGP Chain D 27–474（448 aa） Fragment：DEGP Chain E 27–474（448 aa） Fragment：DEGP Chain F 27–474（448 aa） Fragment：DEGP Chain G 27–474（448 aa） Fragment：DEGP Chain H 27–474（448 aa） Fragment：DEGP Chain I 27–474（448 aa） Fragment：DEGP Chain J 27–474（448 aa） Fragment：DEGP Chain K 27–474（448 aa） Fragment：DEGP Chain L 27–474（448 aa） Fragment：DEGP	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 300MM NACL, 50MM HEPES- NAOH；pH 8；300MM NACL, 50MM HEPES- NAOH cryo-EM vitrification conditions Cryogen ETHANE；EMBEDDED IN VITREOUS ICE USING C-FLAT HOLEY CARBON GRIDS AND A VITROBOT AT 20C.	Resolution 28.00 Å
6JJK Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 35–474（440 aa） Chain B 35–474（440 aa） Chain C 35–474（440 aa） Chain D 35–474（440 aa） Chain E 35–474（440 aa） Chain F 35–474（440 aa）	Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；10% PEG3350 and 0.1 M tacsimate pH 3.4	Resolution 3.60 Å R-free 0.265
6JJL Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 35–474（440 aa） Chain B 35–474（440 aa） Chain C 35–474（440 aa） Chain D 35–474（440 aa） Chain E 35–474（440 aa） Chain F 35–474（440 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；11% PEG3350, 0.1 M tacsimate pH 3.5	Resolution 4.20 Å R-free 0.326
6JJO Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 27–474（448 aa） Chain B 27–474（448 aa） Chain C 27–474（448 aa） Chain D 27–474（448 aa） Chain E 27–474（448 aa） Chain F 27–474（448 aa）	Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；11% PEG3350 and 0.1 M tacsimate pH 3.5	Resolution 4.16 Å R-free 0.278
8F0A Client-bound structure of a DegP trimer within a 12mer cage Deposited 2022-11-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.60 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 12.10 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 13.80 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 90 PDB declaration: 90-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 14.10 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 180 PDB declaration: 180-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å

18 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DEGP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–448； UniProt 27–474 Author chain B； PDBConstruct 1–448； UniProt 27–474 Author chain C； PDBConstruct 1–448； UniProt 27–474 Author chain D； PDBConstruct 1–448； UniProt 27–474 Author chain E； PDBConstruct 1–448； UniProt 27–474 Author chain F； PDBConstruct 1–448； UniProt 27–474

Lysozyme C

Gallus gallus

UniProt B8YK79

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 heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain G； UniProt 36–76 Chain H； UniProt 36–76 Chain I； UniProt 36–76 Chain J； UniProt 36–76 Chain K； UniProt 36–76 Chain L； UniProt 36–76	Fragment：a model peptide substrate Mutation：C30S	Protease do × 12 （P0C0V0）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.6；291 K；65 mM citric acid, 35 mM Bis-Tris propane, 8% PEG3350, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K	Resolution 3.76 Å R-free 0.251

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3OTP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5A3Z Structure of monoclinic Lysozyme obtained by multi crystal data collection Deposited 2015-06-04	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 1–147（147 aa）	Not recorded	NO3 NITRATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.59 Å R-free 0.265
5A3Z Structure of monoclinic Lysozyme obtained by multi crystal data collection Deposited 2015-06-04	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 1–147（147 aa）	Not recorded	NO3 NITRATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.59 Å R-free 0.265
6PBB Crystal structure of Hen Egg White Lysozyme in complex with I3C Deposited 2019-06-13	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 19–147（129 aa）	Not recorded	I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；289 K；0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350	Resolution 1.89 Å R-free 0.240
6PL9 Adduct formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidaz ol-2-ylidene)(eta5-pentamethylcyclopentadienyl)rhodium(III) with HEWL Deposited 2019-06-30	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 19–147（129 aa）	Not recorded	ORS dichloro[(1,2,3,4,5-eta)-pentamethylcyclopentadienyl]rhodium × 1 R1N 2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-rhodapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Rh(III)(Cp*)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.09 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7	Resolution 1.20 Å R-free 0.203
6PLA Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)osmium(II) with HEWL Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–147（129 aa）	Not recorded	NA SODIUM ION × 1 O1N dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)osmium(II) × 2 OS OSMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Os(II)(cymene)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.04 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7	Resolution 1.25 Å R-free 0.184
6PLB Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimida zol-2-ylidene)(eta5-pentamethylcyclopentadienyl)iridium(III) with HEWL Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–147（129 aa）	Not recorded	OT1 2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Ir(III)(Cp*)(1,3-dimethylbenzimidazol-2-ylidene)(chlorido)2 (1.13 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7	Resolution 1.30 Å R-free 0.190
6W7P Crystal Structure Analysis of Space-grown Lysozyme - Ground experiment Deposited 2020-03-19	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 19–147（129 aa）	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 4.6；296 K；PEG 6000, NaCl, Na Acetate	Resolution 1.60 Å R-free 0.220
6W8E Crystal Structure Analysis of Space-grown Lysozyme Deposited 2020-03-20	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 19–147（129 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 4.6；296 K；PEG 6000, NaCl, Na Acetate	Resolution 2.68 Å R-free 0.306
6WEB Multi-Hit SFX using MHz XFEL sources Deposited 2020-04-01	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 19–147（129 aa）	Not recorded	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 3.5；293 K；NaCl, ethylene glycol, PEG 3350, acetate buffer pH 3.5	Resolution 2.10 Å R-free 0.216
6WEC Multi-Hit SFX using MHz XFEL sources Deposited 2020-04-01	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 19–147（129 aa）	Not recorded	CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 5 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 3.5；293 K；NaCl, ethylene glycol, PEG 3350, acetate buffer pH 3.5	Resolution 2.10 Å R-free 0.299
6WGO The interaction of dichlorido(3-(anthracen-9-ylmethyl)-1-methylimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) with HEWL after 1 week Deposited 2020-04-06	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 19–147（129 aa）	Not recorded	NA SODIUM ION × 1 ACT ACETATE ION × 2 U0J {(2R)-1-[(anthracen-9-yl)methyl]-3-methyl-2,3-dihydro-1H-imidazol-2-yl}(dichloro)ruthenium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride	Resolution 1.30 Å R-free 0.192
6WRL The interaction of chlorido(1,5-cyclooctadiene)([4-(2-((tert-butoxycarbonyl)amino)-3-methoxy-3-oxopropyl)-1,3-dimethyl-1H-imidazol-3-ide])rhodium(I) with HEWL after 1 week Deposited 2020-04-29	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 19–147（129 aa）	Not recorded	NA SODIUM ION × 1 ACT ACETATE ION × 3 RH Rhodium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride	Resolution 1.35 Å R-free 0.215
6WRM The interaction of chlorido(1,5-cyclooctadiene)([4-(2-((tert-butoxycarbonyl)amino)-3-methoxy-3-oxopropyl)-1,3-dimethyl-1H-imidazol-3-ide])rhodium(I) with HEWL after 1 month Deposited 2020-04-29	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 19–147（129 aa）	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 2 RH Rhodium × 1 U8G (4-{2-[(tert-butoxycarbonyl)amino]-3-methoxy-3-oxopropyl}-1,3-dimethyl-2,3-dihydro-1H-imidazol-2-yl)rhodium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride	Resolution 1.55 Å R-free 0.249
6WX5 Adducts formed after 3 weeks in the reaction of chlorido[chlorido(2,2'-((2-([2,2':6',2''-Terpyridin]-4'-yloxy)ethyl)azanediyl)bis(ethan-1-ol))platinum(II)] with HEWL Deposited 2020-05-09	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 19–147（129 aa）	Not recorded	NA SODIUM ION × 1 ACT ACETATE ION × 1 PT PLATINUM (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；291 K；0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride pH 4.7	Resolution 1.30 Å R-free 0.202
7D0W Crystal structure of Hen Egg White Lysozyme Deposited 2020-09-12	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 19–147（129 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298.15 K；PEG 3000, TRIS pH 5.6	Resolution 1.80 Å R-free 0.226

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B8YK79_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 4–44； UniProt 36–76 Author chain H； PDBConstruct 4–44； UniProt 36–76 Author chain I； PDBConstruct 4–44； UniProt 36–76 Author chain J； PDBConstruct 4–44； UniProt 36–76 Author chain K； PDBConstruct 4–44； UniProt 36–76 Author chain L； PDBConstruct 4–44； UniProt 36–76

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3otp
Deposition date deposition_date	2010-09-13
Structure title title	Crystal structure of the DegP dodecamer with a model substrate
Keywords keywords	typsin-like protease domain PDZ domains, protease, 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	51.74 Å
Radius of gyration Rg (electron density) rg_electron	51.34 Å
Forward intensity I(0) i0	870364000.00
Molecular weight molecular_weight	243170.0 kDa
Excluded volume excluded_volume	304240 Å³
Envelope volume envelope_volume	506190 Å³
Hydration-shell volume shell_volume	81275 Å³
Envelope diameter envelope_diameter	160.5 Å
Shell Rg shell_rg	58.33 Å
Envelope Rg envelope_rg	48.60 Å
Shape Rg shape_rg	51.32 Å
Total Rg total_rg	51.66 Å
Total atoms total_atoms	17037
Residues n_residues	2375
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	155.7 Å
Rg (real space) rg_real	51.57 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	8.7040e+08
I(0) uncertainty (real space) i0_real_error	1.7120e+07
Rg (reciprocal space) rg_reciprocal	51.86 Å
I(0) (reciprocal space) i0_reciprocal	870700000.0000
Solution quality estimate total_estimate	0.8718
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	77.8 Å
Skewness Skewness skewness	0.003
Kurtosis Kurtosis kurtosis	-0.796
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	52660000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.416

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protease do
Molecular weight formula_weight	48137.3 kDa
EC 编号 ec_number	3.4.21.-
Mutation mutation	S210A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17037

AETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLMQAAALEHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Lysozyme C
Molecular weight formula_weight	4808.0 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	C30S
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

GTGDNYRGYSLGNWVSAAKFESNFNTQATNRNTDGSTDYGILQI

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

▼

7. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

Domain ID domain_id	3otpA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3otpA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3otpB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3otpB03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpB04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3otpC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3otpC03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpC04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3otpD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpD03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpE01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3otpE02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3otpE03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpE04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpF01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3otpF02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3otpF03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	215.427 Å
Unit-cell length b length_b	122.758 Å
Unit-cell length c length_c	138.739 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.760 Å
Low-resolution limit resolution_low	14.991 Å
R factor r_factor	0.2202
R_work r_work	0.2187
R_free r_free	0.2506

fit	/app/data/saxs_computation/ot/3otp/3otp.fit
pddf	/app/data/pr_computation/ot/3otp/3otp.pr.out
profile	/app/data/saxs_computation/ot/3otp/3otp.dat

Crystal structure of the DegP dodecamer with a model substrate

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

Protease do

State in the Current Structure

Other States of the Same Protein in the Database

Lysozyme C

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)