5zkp

Crystal structure of the human platelet-activating factor receptor in complex with SR 27417

Method: X-RAY DIFFRACTION D_max: 105.6 Å Quality: REASONABLE

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

Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor

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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–148	Mutation：F116Y, N169D,P2A, Y98W,A230D, V234A, D289N	9ER N1,N1-dimethyl-N2-[(pyridin-3-yl)methyl]-N2-{4-[2,4,6-tri(propan-2-yl)phenyl]-1,3-thiazol-2-yl}ethane-1,2-diamine × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；HEPES, PEG 400, NaSCN, Na citrate	Resolution 2.81 Å R-free 0.259

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 5ZKP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AKQ D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS Deposited 1997-03-27	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 2–148（147 aa）	Mutation：D95A	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 60-70% A.S., 100MM TRIS-HCL, PH=7.0.	Resolution 1.90 Å R-free 0.240
1AKR G61A OXIDIZED FLAVODOXIN MUTANT Deposited 1997-05-27	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 2–148（147 aa）	Mutation：G61A	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；60-70% AMMONIUM SULFATE, 100MM TRIS-HCL, pH 7.0	Resolution 1.58 Å
1AKT G61N OXIDIZED FLAVODOXIN MUTANT Deposited 1997-05-27	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 2–148（147 aa）	Mutation：G61N	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；60-70% AMMONIUM SULFATE, 100MM TRIS-HCL, pH 7.0	Resolution 1.80 Å
1AKU D95A HYDROQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS Deposited 1997-05-27	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 2–148（147 aa）	Mutation：D95A	SO4 SULFATE ION × 2 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；60-70% AMMONIUM SULFATE, 100MM TRIS-HCL, PH=7.0.	Resolution 1.90 Å R-free 0.270
1AKV D95A SEMIQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS Deposited 1997-05-27	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 2–148（147 aa）	Mutation：D95A	SO4 SULFATE ION × 4 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；60-70% AMMONIUM SULFATE, 100MM TRIS-HCL, PH=7.0.	Resolution 2.00 Å R-free 0.250
1AKW G61L OXIDIZED FLAVODOXIN MUTANT Deposited 1997-05-27	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 2–148（147 aa）	Mutation：G61L	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；60-70% AMMONIUM SULFATE, 100MM TRIS-HCL, pH 7.0	Resolution 1.75 Å R-free 0.194
1AZL G61V FLAVODOXIN MUTANT FROM DESULFOVIBRIO VULGARIS Deposited 1997-11-18	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 2–148（147 aa）	Mutation：G61V	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 7；PROTEIN SEED CRYSTALS WERE OBTAINED FROM 60-70% AMMONIUM SULFATE, 10MM TRIS PH 7.0, 1-2% ACETONE. MACROSEEDS WERE TRANSFERRED TO THE ABOVE SOLUTION WITH NO ACETONE PRESENT., macroseeding	Resolution 1.80 Å
1BU5 X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX Deposited 1998-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain not uniquely mapped Reference range not declared Chain A 2–148（147 aa）	Not recorded	SO4 SULFATE ION × 2 RBF RIBOFLAVIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 CONTAINING 1MM EDTA WITH A PROTEIN CONCENTRATION OF 10-15MG/ML. CRYSTALS APPEAR OVER 1-3 DAYS., pH 7.0	Resolution 1.83 Å R-free 0.202
1C7E D95E HYDROQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS Deposited 2000-02-16	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 2–148（147 aa）	Mutation：D95E	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；70-73% A.S., 210MM TRIS-HCL, 200MM SODIUM ACETATE PH=8.5	Resolution 2.25 Å R-free 0.297
1C7E D95E HYDROQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS Deposited 2000-02-16	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 2–148（147 aa）	Mutation：D95E	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；70-73% A.S., 210MM TRIS-HCL, 200MM SODIUM ACETATE PH=8.5	Resolution 2.25 Å R-free 0.297
1C7F D95E OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS Deposited 2000-02-11	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 2–148（147 aa）	Mutation：YES	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；70-70% A.S. 210MM TRIS-HCL PH=6.5, 200MM SODIUM ACETATE	Resolution 2.00 Å R-free 0.240
1C7F D95E OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS Deposited 2000-02-11	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 2–148（147 aa）	Mutation：YES	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；70-70% A.S. 210MM TRIS-HCL PH=6.5, 200MM SODIUM ACETATE	Resolution 2.00 Å R-free 0.240
1F4P Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS) Deposited 2000-06-08	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 2–148（147 aa）	Mutation：Y98W	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；292 K；Ammonium Sulfate, Tris Buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 292.K	Resolution 1.30 Å R-free 0.169
1FX1 A CRYSTALLOGRAPHIC STRUCTURAL STUDY OF THE OXIDATION STATES OF DESULFOVIBRIO VULGARIS FLAVODOXIN Deposited 1984-10-15	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 1–148（148 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1I1O ROOM TEMPERATURE CRYSTAL STRUCTURE FLAVODOXIN D. VULGARIS MUTANT Y98H AT 2.0 ANG. RESOLUTION Deposited 2001-02-02	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 2–148（147 aa） Fragment：MAIN CHAIN	Mutation：Y98H	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；3.2 M Ammonium Sulfate, Tris.buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å
1J8Q Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris Wild-type at 1.35 Angstrom Resolution Deposited 2001-05-22	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 2–148（147 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Ammonium Sulphate, Tris HCl Buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.35 Å R-free 0.181
1J9E Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris S35C Mutant at 1.44 Angstrom Resolution Deposited 2001-05-25	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 2–148（147 aa）	Mutation：S35C	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Ammonium sulphate, tris-HCl buffer, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.44 Å R-free 0.156
1J9G Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris S64C Mutant, monomer oxidised, at 2.4 Angstrom Resolution Deposited 2001-05-25	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 2–148（147 aa）	Mutation：S64C	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Ammonium Sulphate, Tris HCl Buffer, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.247
1WSB Flavodoxin mutant- S64C Deposited 2004-11-05	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 1–148（148 aa）	Mutation：S64C	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；temperature 298K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.80 Å R-free 0.249
1WSW Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, dimer, semiquinone state Deposited 2004-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Mutation：S64C	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Ammonium Sulphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.69 Å R-free 0.245
1XT6 S35C Flavodoxin Mutant in the semiquinone state Deposited 2004-10-21	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 2–148（147 aa）	Mutation：S35C	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop, vapor diffusion；pH 7；298 K；3.2M ammonium sulfate, pH 7, sitting drop, vapor diffusion, temperature 298K	Resolution 1.80 Å R-free 0.261
1XYV Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, monomer, semiquinone state Deposited 2004-11-11	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 1–148（148 aa）	Mutation：S64C	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Ammonium Sulphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.79 Å R-free 0.237
1XYY Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, homodimer, oxidised state Deposited 2004-11-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Mutation：S64C	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Ammonium Sulphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.70 Å R-free 0.253
2FX2 COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE OXIDATION STATES AT CRYOGENIC TEMPERATURES Deposited 1991-10-17	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 3–148（146 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
3FX2 COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE OXIDATION STATES AT CRYOGENIC TEMPERATURES Deposited 1991-10-17	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 3–148（146 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
4FX2 COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE OXIDATION STATES AT CRYOGENIC TEMPERATURES Deposited 1991-10-17	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 3–148（146 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
5FX2 COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE OXIDATION STATES AT CRYOGENIC TEMPERATURES Deposited 1991-10-17	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 3–148（146 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
5TGZ Crystal Structure of the Human Cannabinoid Receptor CB1 Deposited 2016-09-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–148（147 aa） Fragment：UNP RESIDUES 99-306,UNP RESIDUES 2-148,UNP RESIDUES 332-414	Mutation：T210A, E273K, T283V,P1002A, Y1098W,R340E	ZDG 4-[4-[2-(2,4-dichlorophenyl)-4-methyl-5-(piperidin-1-ylcarbamoyl)pyrazol-3-yl]phenyl]but-3-ynyl nitrate × 1 FMN FLAVIN MONONUCLEOTIDE × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 OLA OLEIC ACID × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；0.1M HEPES pH 7.0-7.4, 100mM (NH4)2HPO4, 25%-32% PEG 400, 2-20 mM Ethylenediaminetetraacetic acid disodium salt dehydrate (EDTA)	Resolution 2.80 Å R-free 0.238
5V56 2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation) in complex with TC114 Deposited 2017-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–148（147 aa） Fragment：UNP RESIDUES 53-433,444-558 Chain B 2–148（147 aa） Fragment：UNP RESIDUES 53-433,444-558	Mutation：E194E, P2A, Y98W Mutation：E194E, P2A, Y98W	836 N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-2-(trifluoromethyl)benzamide × 2 FMN FLAVIN MONONUCLEOTIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM Sodium citrate tribasic dihydrate pH 5.0, 36% (v/v) PEG400, 50-200 mM Ammonium nitrate	Resolution 2.90 Å R-free 0.239
5V57 3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114 Deposited 2017-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–148（147 aa） Fragment：UNP RESIDUES 58-433,444-558 Chain B 2–148（147 aa） Fragment：UNP RESIDUES 58-433,444-558	Mutation：P2A, Y98W Mutation：P2A, Y98W	836 N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-2-(trifluoromethyl)benzamide × 2 FMN FLAVIN MONONUCLEOTIDE × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5；293 K；100 mM Sodium citrate tribasic dihydrate pH 5.0, 36% (v/v) PEG 400, 50-200 mM Ammonium nitrate	Resolution 3.00 Å R-free 0.240
5XR8 Crystal structure of the human CB1 in complex with agonist AM841 Deposited 2017-06-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–148（146 aa） Fragment：;UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,UNP residues 99-306,UNP residues 3-148,UNP residues 332-414 ;	Mutation：T210A,E273K,T283V,Y1098W,R340E	FMN FLAVIN MONONUCLEOTIDE × 1 8D0 (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol × 1 CLR CHOLESTEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.2；293 K；0.1 M sodium cacodylate trihydrate pH 6.2, 120 mM C6H5Na3O7, 30% PEG400 and 100 mM Glycine	Resolution 2.95 Å R-free 0.274
5XRA Crystal structure of the human CB1 in complex with agonist AM11542 Deposited 2017-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–148（146 aa） Fragment：UNP residues 99-306,UNP residues 3-148,UNP residues 332-414	Mutation：T210A, E273K, T283V,Y1098W,R340E	FMN FLAVIN MONONUCLEOTIDE × 1 8D3 (6aR,10aR)-3-(8-bromanyl-2-methyl-octan-2-yl)-6,6,9-trimethyl-6a,7,10,10a-tetrahydrobenzo[c]chromen-1-ol × 1 OLA OLEIC ACID × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 1 CLR CHOLESTEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；0.1 M sodium cacodylate trihydrate pH 6.4, 300-350 mM C4H4KNaO6, 30% PEG400	Resolution 2.80 Å R-free 0.252
5YOB Crystal Structure of flavodoxin without engineered disulfide bond Deposited 2017-10-27	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 3–148（146 aa）	Mutation：Y98W	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Tris-HCL 0.1M Ammonium Sulfate 3.2M	Resolution 1.14 Å R-free 0.177
5YOC Crystal Structure of flavodoxin with engineered disulfide bond C102-R125C Deposited 2017-10-27	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 3–148（146 aa）	Mutation：R125C, Y98W	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Tris-HCL 0.1M Ammonium Sulfa 3.1M	Resolution 1.50 Å R-free 0.192
5YOE Crystal Structure of flavodoxin with engineered disulfide bond A43C-L74C Deposited 2017-10-27	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 3–148（146 aa）	Mutation：A43C, L74C, Y98W	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Tris-HCL 0.1M Ammonium Sulfate 3.2M	Resolution 1.35 Å R-free 0.181
5YOG Crystal Structure of flavodoxin with engineered disulfide bond N14C-C93 Deposited 2017-10-27	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 3–148（146 aa）	Mutation：N14C, Y98W	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；Tris-HCL buffer, pH 7.3 Ammonium Sulfate 3.1M	Resolution 1.42 Å R-free 0.180
6LI0 Crystal structure of GPR52 in complex with agonist c17 Deposited 2019-12-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–148（146 aa）	Mutation：A130W,Y1098W,A264L,W278Q,C314P,S318A,N321D,V323T	EN6 N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide × 1 FMN FLAVIN MONONUCLEOTIDE × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 17 PEG DI(HYDROXYETHYL)ETHER × 8 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5；293 K；0.13-0.18 M sodium acetate, 0.1 M sodium citrate PH5.0, 32-35% PEG400	Resolution 2.20 Å R-free 0.220
6LI1 Crystal structure of GPR52 ligand free form with flavodoxin fusion Deposited 2019-12-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–148（146 aa）	Mutation：A130W,Y1098W,W278Q,C314P,S318A,N321D,V323T	OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 FMN FLAVIN MONONUCLEOTIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5；293 K；0.1 M potassium acetate, 0.1 M sodium citrate pH 5.0, and 30% PEG400	Resolution 2.90 Å R-free 0.267
7DDZ The Crystal Structure of Human Neuropeptide Y Y2 Receptor with JNJ-31020028 Deposited 2020-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–148（146 aa）	Not recorded	H46 ~{N}-[4-[4-[(1~{S})-2-(diethylamino)-2-oxidanylidene-1-phenyl-ethyl]piperazin-1-yl]-3-fluoranyl-phenyl]-2-pyridin-3-yl-benzamide × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；0.1 M HEPES, pH 7.0-7.5, 250-350 mM (NH4)2SO4, and 20-30% PEG500DME, or 0.1 M MES, pH 6.0-6.5, 380-420 mM NH4 tartrate, and 24-26% PEG500DME	Resolution 2.80 Å R-free 0.289
7K15 Crystal structure of the Human Leukotriene B4 Receptor 1 in Complex with Selective Antagonist MK-D-046 Deposited 2020-09-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–148（147 aa）	Not recorded	VRJ N-(tert-butylsulfonyl)-4-fluoro-2-{(3S,4R)-4-hydroxy-3-[(pyridin-2-yl)methyl]-3,4-dihydro-2H-1-benzopyran-7-yl}benzamide × 1 NA SODIUM ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1 OLA OLEIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 1PE PENTAETHYLENE GLYCOL × 1 2PE NONAETHYLENE GLYCOL × 1 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.8；293 K；sodium citrate tribasic dihydrate pH 5.8, sodium acetate trihydrate, benzamidine hydrochloride, PEG-400, MK-D-046, DMSO	Resolution 2.88 Å R-free 0.261
7V3Z Structure of cannabinoid receptor type 1(CB1) Deposited 2021-08-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–148（146 aa）	Mutation：H154L,T210A,E273K,T283V,Y1098W,R340E	9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 CLR CHOLESTEROL × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.2；293.15 K；30% PEG400, 100 mM HEPES sodium pH 7.2, 80-100mM sodium citrate tribasic dihydrate	Resolution 3.29 Å R-free 0.276

39 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FLAV_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 219–365； UniProt 2–148

Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor

Homo sapiens

UniProt P25105

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–216 Chain A； UniProt 224–316	Mutation：F116Y, N169D,P2A, Y98W,A230D, V234A, D289N	9ER N1,N1-dimethyl-N2-[(pyridin-3-yl)methyl]-N2-{4-[2,4,6-tri(propan-2-yl)phenyl]-1,3-thiazol-2-yl}ethane-1,2-diamine × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；HEPES, PEG 400, NaSCN, Na citrate	Resolution 2.81 Å R-free 0.259

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5ZKP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5ZKQ Crystal structure of the human platelet-activating factor receptor in complex with ABT-491 Deposited 2018-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–218（217 aa） Chain A 224–316（93 aa） Chain B 2–218（217 aa） Chain B 224–316（93 aa）	Mutation：F116Y, N169D, A230D,C97A, I137R, A230D, V234A, D289N Mutation：F116Y, N169D, A230D,C97A, I137R, A230D, V234A, D289N Mutation：F116Y, N169D, A230D,C97A, I137R, A230D, V234A, D289N Mutation：F116Y, N169D, A230D,C97A, I137R, A230D, V234A, D289N	9EU 4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 7 ZN ZINC ION × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；HEPES, PEG 400, MgSO4	Resolution 2.90 Å R-free 0.235
8XYD Structure of Platelet-activating factor receptor-G protein complex bound to platelet-activating factor Deposited 2024-01-19	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 × 5 PDB declaration: pentameric	Chain A 1–342（342 aa）	Not recorded	PFS (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTAFR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–218； UniProt 2–216 Author chain A； PDBConstruct 366–458； UniProt 224–316

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	5zkp
Deposition date deposition_date	2018-03-25
Structure title title	Crystal structure of the human platelet-activating factor receptor in complex with SR 27417
Keywords keywords	G protein-coupled receptor, Platelet-activating factor receptor, Complex, SIGNALING PROTEIN; SIGNALING PROTEIN
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	30.64 Å
Radius of gyration Rg (electron density) rg_electron	29.80 Å
Forward intensity I(0) i0	35460100.00
Molecular weight molecular_weight	48888.0 kDa
Excluded volume excluded_volume	62145 Å³
Envelope volume envelope_volume	78579 Å³
Hydration-shell volume shell_volume	24653 Å³
Envelope diameter envelope_diameter	111.5 Å
Shell Rg shell_rg	33.17 Å
Envelope Rg envelope_rg	29.66 Å
Shape Rg shape_rg	29.84 Å
Total Rg total_rg	30.02 Å
Total atoms total_atoms	3450
Residues n_residues	436
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	105.6 Å
Rg (real space) rg_real	31.06 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	3.5460e+07
I(0) uncertainty (real space) i0_real_error	5.6190e+05
Rg (reciprocal space) rg_reciprocal	30.88 Å
I(0) (reciprocal space) i0_reciprocal	35460000.0000
Solution quality estimate total_estimate	0.5739
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.545
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9954000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.584; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.386; Smooth: 0.740

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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	Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor
Molecular weight formula_weight	52430.5 kDa
Mutation mutation	F116Y, N169D,P2A, Y98W,A230D, V234A, D289N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3455

GAPEPHDSSHMDSEFRYTLFPIVYSIIFVLGVIANGYVLWVFARLYPCKKFNEIKIFMVNLTMADMLFLITLPLWIVYYQNQGNWILPKFLCNVAGCLFFINTYCSVAFLGVITYNRYQAVTRPIKTAQANTRKRGISLSLVIWVAIVGAASYFLILDSTNTVPDSAGSGDVTRCFEHYEKGSVPVLIIHIFIVFSFFLVFLIILFCNLVIIRTLLMQAKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSWEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAIAEVKRRDLWMACTVLAVFIICFVPHHVVQLPWTLAELGFQDSKFHQAINDAHQVTLCLLSTNCVLNPVIYCFLTKKFRKHLTEKFYSMRSSRKEFLEVLFQ

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	N1,N1-dimethyl-N2-[(pyridin-3-yl)methyl]-N2-{4-[2,4,6-tri(propan-2-yl)phenyl]-1,3-thiazol-2-yl}ethane-1,2-diamine
Molecular weight formula_weight	464.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	67.050 Å
Unit-cell length b length_b	67.050 Å
Unit-cell length c length_c	280.250 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	6

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

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2240
R_work r_work	0.2220
R_free r_free	0.2590

fit	/app/data/saxs_computation/zk/5zkp/5zkp.fit
pddf	/app/data/pr_computation/zk/5zkp/5zkp.pr.out
profile	/app/data/saxs_computation/zk/5zkp/5zkp.dat

Crystal structure of the human platelet-activating factor receptor in complex with SR 27417

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

Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor

State in the Current Structure

Other States of the Same Protein in the Database

Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)