6sze

RIP2 Kinase Catalytic Domain complex with 5-Amino-1-Phenylpyrazole-4-Carboxamide.

Method: X-RAY DIFFRACTION D_max: 90.3 Å Quality: GOOD

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

Receptor-interacting serine/threonine-protein kinase 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–310 Chain B； UniProt 1–310	Not recorded	M2B 5-Amino-1-Phenylpyrazole-4-Carboxamide × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100mM buffer (Mes or Hepes pH6.8-7.5), 12-28% PEG 400, 50-250mM CaCl2, 0-200mM NaCl	Resolution 2.94 Å R-free 0.234

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 6SZE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N7Z Solution structure of RIP2 CARD Deposited 2015-09-28	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 A 434–539（106 aa） Fragment：UNP residues 434-539	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 301 K；Pressure ambient NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] CARD-1, 50 mM [U-98% 2H] DTT-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N83 p75NTR DD:RIP2 CARD Deposited 2015-10-02	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 × 2 PDB declaration: dimeric	Chain B 434–539（106 aa） Fragment：UNP residues 435-539	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 301 K；Pressure ambient NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] p75NTR DD-1, 10 mM [U-98% 2H] DTT-2, 1 mM RIP2 CARD-3, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] RIP2 CARD-4, 1 mM p75NTR DD-5, 10 mM [U-98% 2H] DTT-6, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4C8B Structure of the kinase domain of human RIPK2 in complex with ponatinib Deposited 2013-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–317（310 aa） Fragment：KINASE DOMAIN, RESIDUES 8-317 Chain B 8–317（310 aa） Fragment：KINASE DOMAIN, RESIDUES 8-317	Not recorded	0LI 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 16% PEG3350, 0.1M AMMONIUM CITRATE	Resolution 2.75 Å R-free 0.244
5AR2 RIP2 Kinase Catalytic Domain (1 - 310) Deposited 2015-09-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310 Chain B 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；28% PEG400, 5% GLYCEROL, 0.1M HEPES PH7.5, 0.2M CACL2	Resolution 2.44 Å R-free 0.211
5AR3 RIP2 Kinase Catalytic Domain (1 - 310) complex with AMP-PCP Deposited 2015-09-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310 Chain B 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310	Not recorded	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 20% PEG3350, 0.2M NAKTARTRATE	Resolution 3.23 Å R-free 0.254
5AR4 RIP2 Kinase Catalytic Domain (1 - 310) complex with SB-203580 Deposited 2015-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310 Chain B 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310	Not recorded	SB2 4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-3H-IMIDAZOL-4-YL]-PYRIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1M TRIS HCL PH8.5, 0.7M DINH4TARTRATE.	Resolution 2.70 Å R-free 0.216
5AR5 RIP2 Kinase Catalytic Domain (1 - 310) complex with Benzimidazole Deposited 2015-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310 Chain B 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310	Not recorded	CA CALCIUM ION × 1 IQ7 2-(2-(4-CHLOROPHENYL)-1H-IMIDAZOL-5-YL)-N,1-BIS(2-METHOXYETHYL)-1H-BENZO[D]IMIDAZOLE-5-CARBOXAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.2M CACL2, 5% GLYCEROL, 0.1M HEPES PH 7.5, 26.6% PEG400	Resolution 2.66 Å R-free 0.217
5AR7 RIP2 Kinase Catalytic Domain (1 - 310) complex with Biaryl Urea Deposited 2015-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310 Chain B 1–310（310 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 1-310	Not recorded	SR8 1-(5-TERT-BUTYL-1,2-OXAZOL-3-YL)-3-(4-PYRIDIN-4-YLOXYPHENYL)UREA × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；30% PEG300, 0.1M MES PH6.5	Resolution 2.71 Å R-free 0.225
5AR8 RIP2 Kinase Catalytic Domain (1 - 310) complex with Biphenylsulfonamide Deposited 2015-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：KINASE DOMAIN, RESIDUES 1-310 Chain B 1–310（310 aa） Fragment：KINASE DOMAIN, RESIDUES 1-310	Not recorded	XYW 2,6-bis(fluoranyl)-N-[3-[5-[2-[(3-methylsulfonylphenyl)amino]pyrimidin-4-yl]-2-morpholin-4-yl-1,3-thiazol-4-yl]phenyl]benzenesulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；30% GLYCEROL, 0.07M NA OAC PH4.6, 1.4M NA FORMATE	Resolution 2.79 Å R-free 0.233
5J79 The identification and pharmacological characterization of 6-(tert-butylsulfonyl)-N-(5-fluoro-1H-indazol-3-yl)quinolin-4-amine (GSK583), a highly potent and selective inhibitor of RIP2 Kinase, Compound 3 complex Deposited 2016-04-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：UNP residues 1-310 Chain B 1–310（310 aa） Fragment：UNP residues 1-310	Not recorded	6GE 4-methyl-3-{[6-(methylsulfonyl)quinolin-4-yl]amino}phenol × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5M Ammonium sulphate, 25% glycerol	Resolution 2.69 Å R-free 0.219
5J7B The identification and pharmacological characterization of 6-(tert-butylsulfonyl)-N-(5-fluoro-1H-indazol-3-yl)quinolin-4-amine (GSK583), a highly potent and selective inhibitor of RIP2 Kinase, GSK583 complex Deposited 2016-04-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Fragment：UNP residues 1-310 Chain B 1–310（310 aa） Fragment：UNP residues 1-310	Not recorded	6GD 6-(tert-butylsulfonyl)-N-(5-fluoro-2H-indazol-3-yl)quinolin-4-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；100mM Mes pH7, 12% PEG 400, 250mM CaCl2. Crystals soaked in compound for 2 hours.	Resolution 2.53 Å R-free 0.233
5NG0 Structure of RIP2K(L294F) with bound AMPPCP Deposited 2017-03-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–300（300 aa） Chain B 1–300（300 aa）	Not recorded	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Hepes 100 mM pH 7.5, 1 mM MgCl2, 2.0 M LiCl and 5% PEG 6000	Resolution 2.00 Å R-free 0.191
5NG2 Structure of RIP2K(D146N) with bound Staurosporine Deposited 2017-03-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–300（300 aa） Chain B 1–300（300 aa）	Not recorded	STU STAUROSPORINE × 2 PO4 PHOSPHATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；.1 M MES pH6.5, 2M NaCl, 0.1 mM Na(H2PO4), 0.1 mM of K(H2PO4)	Resolution 2.80 Å R-free 0.226
5NG3 Structure of inactive kinase RIP2K(K47R) Deposited 2017-03-16	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 D 1–300（300 aa）	Mutation：K47R Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 0.5 mM (NH4)2SO4	Resolution 2.60 Å R-free 0.269
5NG3 Structure of inactive kinase RIP2K(K47R) Deposited 2017-03-16	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 1–300（300 aa）	Mutation：K47R	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 0.5 mM (NH4)2SO4	Resolution 2.60 Å R-free 0.269
5NG3 Structure of inactive kinase RIP2K(K47R) Deposited 2017-03-16	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 A 1–300（300 aa）	Mutation：K47R Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 0.5 mM (NH4)2SO4	Resolution 2.60 Å R-free 0.269
5NG3 Structure of inactive kinase RIP2K(K47R) Deposited 2017-03-16	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 C 1–300（300 aa）	Mutation：K47R	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 0.5 mM (NH4)2SO4	Resolution 2.60 Å R-free 0.269
5W5J Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–311（310 aa） Chain B 2–311（310 aa）	Not recorded	9WS N-(2-chlorophenyl)pyrazolo[1,5-a]pyridine-3-carboxamide × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；1.6M ammonium sulfate, 0.1M citric acid pH 5.0	Resolution 2.85 Å R-free 0.268
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–311（310 aa） Fragment：UNP residues 2-311 Chain B 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–311（310 aa） Fragment：UNP residues 2-311 Chain D 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 2–311（310 aa） Fragment：UNP residues 2-311 Chain F 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 2–311（310 aa） Fragment：UNP residues 2-311 Chain H 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 2–311（310 aa） Fragment：UNP residues 2-311 Chain J 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 2–311（310 aa） Fragment：UNP residues 2-311 Chain L 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 2–311（310 aa） Fragment：UNP residues 2-311 Chain N 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5W5O Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases. Deposited 2017-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 2–311（310 aa） Fragment：UNP residues 2-311 Chain P 2–311（310 aa） Fragment：UNP residues 2-311	Not recorded	9XA 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.0M lithium chloride, 10.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0	Resolution 2.89 Å R-free 0.252
5YRN Structure of RIP2 CARD domain Deposited 2017-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 434–540（107 aa） Fragment：CARD domain Chain B 434–540（107 aa） Fragment：CARD domain Chain C 434–540（107 aa） Fragment：CARD domain Chain D 434–540（107 aa） Fragment：CARD domain Chain E 434–540（107 aa） Fragment：CARD domain Chain F 434–540（107 aa） Fragment：CARD domain Chain G 434–540（107 aa） Fragment：CARD domain Chain H 434–540（107 aa） Fragment：CARD domain Chain I 434–540（107 aa） Fragment：CARD domain Chain J 434–540（107 aa） Fragment：CARD domain Chain K 434–540（107 aa） Fragment：CARD domain Chain L 434–540（107 aa） Fragment：CARD domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 4.10 Å
6ES0 Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop targeting inhibitor CS-R35 Deposited 2017-10-19	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 3–317（315 aa）	Not recorded	BW8 2-[2-fluoranyl-4-[[2-fluoranyl-4-[2-(methylcarbamoyl)pyridin-4-yl]oxy-phenyl]carbamoylamino]phenyl]sulfanylethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG Smear Low -- 0.1M MES pH 6.5 -- 0.05M magnesium acetate -- 0.05M magnesium chloride	Resolution 2.38 Å R-free 0.258
6ES0 Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop targeting inhibitor CS-R35 Deposited 2017-10-19	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 3–317（315 aa）	Not recorded	BW8 2-[2-fluoranyl-4-[[2-fluoranyl-4-[2-(methylcarbamoyl)pyridin-4-yl]oxy-phenyl]carbamoylamino]phenyl]sulfanylethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG Smear Low -- 0.1M MES pH 6.5 -- 0.05M magnesium acetate -- 0.05M magnesium chloride	Resolution 2.38 Å R-free 0.258
6FU5 Structure of the kinase domain of human RIPK2 in complex with the inhibitor CSLP18 Deposited 2018-02-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–317（315 aa） Chain B 3–317（315 aa）	Not recorded	E7N ~{N}-[5-[2-azanyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]-2-methoxy-phenyl]propane-1-sulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 nL sitting drops containing 50 nL protein and 100 nL of a reservoir solution containing 0.2 M potassium formate and 20% (w/v) PEG3350	Resolution 3.26 Å R-free 0.271
6GFJ Structure of RIP2 CARD domain fused to crystallisable MBP tag Deposited 2018-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 435–540（106 aa） Chain B 435–540（106 aa） Chain C 435–540（106 aa） Chain D 435–540（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.25 M NaNO3, and 22% (w/v) PEG 3350	Resolution 3.30 Å R-free 0.266
6GGS Structure of RIP2 CARD filament Deposited 2018-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 431–540（110 aa） Chain B 431–540（110 aa） Chain C 431–540（110 aa） Chain D 431–540（110 aa） Chain E 431–540（110 aa） Chain F 431–540（110 aa） Chain G 431–540（110 aa） Chain H 431–540（110 aa） Chain I 431–540（110 aa） Chain J 431–540（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
6HMX RIP2 Kinase Catalytic Domain complex with N(4,5dimethyl1Hpyrazol3yl)7methoxy6(2methylpropane2sulfonyl)quinolin4amine Deposited 2018-09-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Chain B 1–310（310 aa）	Not recorded	GEZ 6-~{tert}-butylsulfonyl-~{N}-(3,4-dimethyl-1~{H}-pyrazol-5-yl)-7-methoxy-quinolin-4-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100mM Mes pH7 12% PEG400 250mM CaCl2	Resolution 2.53 Å R-free 0.192
6RN8 RIP2 Kinase Catalytic Domain complex with 2(4[(1,3benzothiazol5yl)amino]6(2methylpropane2sulfonyl)quinazolin7yl)oxy)ethyl phosphate Deposited 2019-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Chain B 1–310（310 aa）	Not recorded	K9T 2-[4-(1,3-benzothiazol-5-ylamino)-6-~{tert}-butylsulfonyl-quinazolin-7-yl]oxyethyl dihydrogen phosphate × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Morpheus G2. 0.1M Carboxylic acids, 0.1M buffer system 1 pH6.5, 50% Precipitant Mix 2	Resolution 2.69 Å R-free 0.212
6RNA RIP2 Kinase Catalytic Domain complex with 2({4[(1,3benzothiazol5yl)amino]6(2methylpropane2sulfonyl)quinazolin7yl}oxy)ethan1ol Deposited 2019-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Chain B 1–310（310 aa）	Not recorded	KA2 2-[4-(1,3-benzothiazol-5-ylamino)-6-~{tert}-butylsulfonyl-quinazolin-7-yl]oxyethanol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100mM Mes pH7, 12% PEG 400, 250mM CaCl2	Resolution 2.62 Å R-free 0.190
6S1F Structure of the kinase domain of human RIPK2 in complex with the inhibitor CSLP3 Deposited 2019-06-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–317（315 aa） Chain B 3–317（315 aa）	Not recorded	KRE ~{N}-[3-[2-azanyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]-5-methoxy-phenyl]methanesulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；150 nL sitting drops containing 100 nL protein and 50 nL of a reservoir solution containing the BCS5 condition 20% PEG Smear High, 0.1M citrate pH 5.5	Resolution 3.11 Å R-free 0.300
6S1F Structure of the kinase domain of human RIPK2 in complex with the inhibitor CSLP3 Deposited 2019-06-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 3–317（315 aa） Chain D 3–317（315 aa）	Not recorded	KRE ~{N}-[3-[2-azanyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]-5-methoxy-phenyl]methanesulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；150 nL sitting drops containing 100 nL protein and 50 nL of a reservoir solution containing the BCS5 condition 20% PEG Smear High, 0.1M citrate pH 5.5	Resolution 3.11 Å R-free 0.300
6SZJ RIP2 Kinase Catalytic Domain complex with 5amino1tertbutyl3(3methoxyphenyl)1H pyrazole4carboxamide. Deposited 2019-10-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–310（310 aa） Chain B 1–310（310 aa）	Not recorded	M5W 5-amino-1-~{tert}-butyl-3-(3-methoxyphenyl)pyrazole-4-carboxamide × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100mM buffer (Mes or Hepes pH6.8-7.5), 12-28% PEG 400, 50-250mM CaCl2, 0-200mM NaCl	Resolution 2.53 Å R-free 0.241
6UL8 RIP2 kinase catalytic domain complex with (5S,6S,8R)-2-(benzo[d]thiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methanopyrazolo[1,5-a][1,3]diazocine-3-carboxamide Deposited 2019-10-07	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 5–310（306 aa）	Mutation：C7S, S168C	Q9J (5S,6S,8R)-2-(1,3-benzothiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methanopyrazolo[1,5-a][1,3]diazocine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；85 mM Tris, pH 7.5, 200 mM calcium chloride, 10% PEG400, 5% glycerol, in 24 well Linbro trays at 22 degrees C. Crystals were frozen directly from the tray using paraffin oil as a cryoprotectant.	Resolution 2.68 Å R-free 0.220
6UL8 RIP2 kinase catalytic domain complex with (5S,6S,8R)-2-(benzo[d]thiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methanopyrazolo[1,5-a][1,3]diazocine-3-carboxamide Deposited 2019-10-07	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 5–310（306 aa）	Mutation：C7S, S168C	Q9J (5S,6S,8R)-2-(1,3-benzothiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methanopyrazolo[1,5-a][1,3]diazocine-3-carboxamide × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；85 mM Tris, pH 7.5, 200 mM calcium chloride, 10% PEG400, 5% glycerol, in 24 well Linbro trays at 22 degrees C. Crystals were frozen directly from the tray using paraffin oil as a cryoprotectant.	Resolution 2.68 Å R-free 0.220
7OBS Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide Deposited 2021-04-23	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 B 530–540（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.095 M Hepes pH7.7, 23%PEG 400, 0.19 M CaCl2 and 5 % Glycerol	Resolution 1.80 Å R-free 0.189
7OBT Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide and stabilizer Fusicoccin-A Deposited 2021-04-23	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 B 530–540（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FSC FUSICOCCIN × 2 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.095 M Hepes pH7.7, 23%PEG 400, 0.19 M CaCl2 and 5 % Glycerol	Resolution 2.30 Å R-free 0.246
8AZA Structure of RIP2K dimer bound to the XIAP BIR2 domain Deposited 2022-09-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8X2O RIPK2 in complex with K252 Deposited 2023-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa） Chain B 1–316（316 aa）	Not recorded	6IL ~{N}-[(1~{R})-4-[4-[(6-fluoranyl-1,3-benzothiazol-5-yl)amino]thieno[2,3-d]pyrimidin-6-yl]cyclohex-3-en-1-yl]cyclopropanecarboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM Mes pH7,12% PEG 400, 250mM CaCl2	Resolution 2.26 Å R-free 0.254
9F3V RIP2K kinase domain dimer with bound compound 37 (N399), a speific NOD1 pathway inhibitor Deposited 2024-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa） Chain B 1–316（316 aa）	Not recorded	A1H90 N-[2,4-bis(chloranyl)-5-methoxy-phenyl]-7-[2-(diethylamino)ethoxy]-6-methoxy-quinazolin-4-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Compound 37, in powder form was solubilized in DMSO at 5 mM concentration. One aliquot of protein at 1.14 mg/ml was thawed and mixed with 50 microM inhibitor and kept on ice for 10 minutes. The complex was than concentrated to 3.8 mg/ml. solutions containing 3.8 mg/ml of protein-inhibitor complex equilibrated against 0.1 M citric acid and 0.8 M sodium formate at pH 5.	Resolution 1.94 Å R-free 0.256

32 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RIPK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–311； UniProt 1–310 Author chain B； PDBConstruct 2–311； UniProt 1–310

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	6sze
Deposition date deposition_date	2019-10-02
Structure title title	RIP2 Kinase Catalytic Domain complex with 5-Amino-1-Phenylpyrazole-4-Carboxamide.
Keywords keywords	;Fragment Based Drug Design (FBDD), Receptor interacting protein 2 kinase, RIPK2, RIP2K, RIP2, Structure based drug design (SBDD), TRANSFERASE ;; TRANSFERASE
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	26.21 Å
Radius of gyration Rg (electron density) rg_electron	25.04 Å
Forward intensity I(0) i0	61495300.00
Molecular weight molecular_weight	63383.0 kDa
Excluded volume excluded_volume	80242 Å³
Envelope volume envelope_volume	96837 Å³
Hydration-shell volume shell_volume	32061 Å³
Envelope diameter envelope_diameter	94.4 Å
Shell Rg shell_rg	32.64 Å
Envelope Rg envelope_rg	25.22 Å
Shape Rg shape_rg	25.05 Å
Total Rg total_rg	25.85 Å
Total atoms total_atoms	4480
Residues n_residues	550
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	90.3 Å
Rg (real space) rg_real	26.19 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	6.1500e+07
I(0) uncertainty (real space) i0_real_error	9.2840e+05
Rg (reciprocal space) rg_reciprocal	26.19 Å
I(0) (reciprocal space) i0_reciprocal	61500000.0000
Solution quality estimate total_estimate	0.8609
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.090
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20800000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Receptor-interacting serine/threonine-protein kinase 2
Molecular weight formula_weight	35683.0 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4646

GMNGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEITFLEAVIQLK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	5-Amino-1-Phenylpyrazole-4-Carboxamide
Molecular weight formula_weight	202.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6szea_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d6szeb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6szeA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	6szeB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	131.660 Å
Unit-cell length b length_b	131.660 Å
Unit-cell length c length_c	107.084 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.940 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1791
R_work r_work	0.1761
R_free r_free	0.2341

fit	/app/data/saxs_computation/sz/6sze/6sze.fit
pddf	/app/data/pr_computation/sz/6sze/6sze.pr.out
profile	/app/data/saxs_computation/sz/6sze/6sze.dat