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6gpx

CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812

Method: X-RAY DIFFRACTION Dmax: 92.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2

Homo sapiens

UniProt P00268

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 1–54 Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ; ZN ZINC ION × 1 OLA OLEIC ACID × 11 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1 X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 6.5；293 K；protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using the IMISX in-situ crystallization plate. 40nl of LCP bolus were dispensed using the Mosquito LCP robot (TTP Labtech) and overlaid with 800 nl of precipitant solution. Crystals were obtained in 0.1 M bis-tris propane pH 6.5, 0.2 M potassium nitrate, 39% (v/v) PEG400, 3% (v/v) 1,2-propanediol Resolution 2.70 Å R-free 0.243
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–54 Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ; OLA OLEIC ACID × 3 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1 X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 6.5；293 K；protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using the IMISX in-situ crystallization plate. 40nl of LCP bolus were dispensed using the Mosquito LCP robot (TTP Labtech) and overlaid with 800 nl of precipitant solution. Crystals were obtained in 0.1 M bis-tris propane pH 6.5, 0.2 M potassium nitrate, 39% (v/v) PEG400, 3% (v/v) 1,2-propanediol Resolution 2.70 Å R-free 0.243

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 6GPX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B13 CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10A MUTANT Deposited 1998-11-26 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 1–54（54 aa）
Mutation：G10A FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4.6.
Resolution 1.50 Å R-free 0.191
1B2J CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G43A MUTANT Deposited 1998-11-27 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 1–54（54 aa）
Mutation：G43A FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4.5., pH 4.6
Resolution 1.60 Å R-free 0.234
1B2O CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10VG43A MUTANT Deposited 1998-11-30 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 1–54（54 aa）
Mutation：G10V, G43A FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLISED FROM 70% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 5.0.
Resolution 1.90 Å R-free 0.237
1B2O CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10VG43A MUTANT Deposited 1998-11-30 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 1–54（54 aa）
Mutation：G10V, G43A FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLISED FROM 70% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 5.0.
Resolution 1.90 Å R-free 0.237
1BE7 CLOSTRIDIUM PASTEURIANUM RUBREDOXIN C42S MUTANT Deposited 1998-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–54（54 aa）
Mutation：C42S FE FE (III) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4., pH 4.0
Resolution 1.65 Å R-free 0.201
1BFY SOLUTION STRUCTURE OF REDUCED CLOSTRIDIUM PASTEURIANUM RUBREDOXIN, NMR, 20 STRUCTURES Deposited 1998-05-23 Different construct 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 1–54（54 aa）
Not recorded FE FE (III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1 M；Pressure NORMAL
NMR sample composition WATER
Resolution not provided
1C09 RUBREDOXIN V44A CP Deposited 1999-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–54（54 aa）
Chain B 1–54（54 aa）
Chain C 1–54（54 aa）
Mutation：V44A Mutation：V44A Mutation：V44A FE FE (III) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；281 K；0.1M Na acetate pH 4.5, 2M ammonium sulfate, temperature 281K
Resolution 1.60 Å
1FHH X-RAY CRYSTAL STRUCTURE OF OXIDIZED RUBREDOXIN Deposited 2000-08-01 Different construct 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 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.50 Å
1FHM X-RAY CRYSTAL STRUCTURE OF REDUCED RUBREDOXIN Deposited 2000-08-02 Different construct 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 1–54（54 aa）
Not recorded FE2 FE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；2M ammonium sulfate, 0.1M sodium acetate, 0.1 g sodium dithionite, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.50 Å
1IRN RUBREDOXIN (ZN-SUBSTITUTED) AT 1.2 ANGSTROMS RESOLUTION Deposited 1995-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 1.20 Å
1IRO RUBREDOXIN (OXIDIZED, FE(III)) AT 1.1 ANGSTROMS RESOLUTION Deposited 1995-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 1.10 Å
1R0F Gallium-substituted rubredoxin Deposited 2003-09-22 Different construct 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 1–54（54 aa）
Not recorded GA GALLIUM (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.60 Å R-free 0.205
1R0G mercury-substituted rubredoxin Deposited 2003-09-22 Different construct 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 1–54（54 aa）
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.60 Å R-free 0.189
1R0H cobalt-substituted rubredoxin Deposited 2003-09-22 Different construct 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 1–54（54 aa）
Not recorded CO COBALT (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.197
1R0I cadmium-substituted rubredoxin Deposited 2003-09-22 Different construct 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 1–54（54 aa）
Not recorded CD CADMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium acetate, ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.50 Å R-free 0.146
1R0J nickel-substituted rubredoxin Deposited 2003-09-22 Different construct 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 1–54（54 aa）
Not recorded NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium acetate, ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.242
1SMM Crystal Structure of Cp Rd L41A mutant in oxidized state Deposited 2004-03-09 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 1–54（54 aa）
Mutation：L41A SO4 SULFATE ION × 1 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；ammonium sulfate, sodium chloride, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.36 Å R-free 0.189
1SMU Crystal Structure of Cp Rd L41A mutant in reduced state 1 (drop-reduced) Deposited 2004-03-09 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 1–54（54 aa）
Mutation：L41A FE2 FE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；ammonium sulfate, sodium dithionite, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.43 Å R-free 0.213
1SMW Crystal Structure of Cp Rd L41A mutant in reduced state 2 (soaked) Deposited 2004-03-09 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 1–54（54 aa）
Mutation：L41A FE2 FE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；ammonium sulfate, sodium chloride, sodium dithionite, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.38 Å R-free 0.200
1T9O Crystal Structure of V44G Cp Rubredoxin Deposited 2004-05-18 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 1–54（54 aa）
Mutation：V44G FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；279 K；ammonium sulfate, acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.00 Å R-free 0.183
1T9O Crystal Structure of V44G Cp Rubredoxin Deposited 2004-05-18 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 1–54（54 aa）
Mutation：V44G FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；279 K；ammonium sulfate, acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.00 Å R-free 0.183
1T9O Crystal Structure of V44G Cp Rubredoxin Deposited 2004-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–54（54 aa）
Mutation：V44G FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；279 K；ammonium sulfate, acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.00 Å R-free 0.183
1T9P Crystal Structure of V44A, G45P Cp Rubredoxin Deposited 2004-05-18 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 1–54（54 aa）
Mutation：V44A, G45P FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.215
1T9P Crystal Structure of V44A, G45P Cp Rubredoxin Deposited 2004-05-18 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 1–54（54 aa）
Mutation：V44A, G45P FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.215
1T9P Crystal Structure of V44A, G45P Cp Rubredoxin Deposited 2004-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–54（54 aa）
Mutation：V44A, G45P FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.215
1T9Q Crystal Structure of V44L Cp Rubredoxin Deposited 2004-05-18 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 1–54（54 aa）
Mutation：V44L FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；ammonium sulfate, acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.228
2PVE NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-09 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 1–54（54 aa）
Mutation：K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；298 K；48% Ammonium Sulphate, 3% Ethanol Glycol, 0.1M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.50
Resolution 0.79 Å R-free 0.125
2PVE NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-09 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 1–54（54 aa）
Mutation：K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；298 K；48% Ammonium Sulphate, 3% Ethanol Glycol, 0.1M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.50
Resolution 0.79 Å R-free 0.125
2PVE NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–54（54 aa）
Mutation：K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；298 K；48% Ammonium Sulphate, 3% Ethanol Glycol, 0.1M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.50
Resolution 0.79 Å R-free 0.125
4MBS Crystal Structure of the CCR5 Chemokine Receptor Deposited 2013-08-19 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 1–54（54 aa） Fragment：Rubredoxin inserted into CCR5 between residue 223 and 227
Mutation：C58Y, G163N, A233D, K303E MRV 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]oct-8-yl}-1-phenylpropyl]cyclohexanecarboxamide × 1 ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；32% PEG 400, 0.1M HEPES, 0.1M sodium chloride, pH 7.0, Lipidic cubic phase, temperature 293K
Resolution 2.71 Å R-free 0.263
4MBS Crystal Structure of the CCR5 Chemokine Receptor Deposited 2013-08-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–54（54 aa） Fragment：Rubredoxin inserted into CCR5 between residue 223 and 227
Mutation：C58Y, G163N, A233D, K303E MRV 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]oct-8-yl}-1-phenylpropyl]cyclohexanecarboxamide × 1 ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；32% PEG 400, 0.1M HEPES, 0.1M sodium chloride, pH 7.0, Lipidic cubic phase, temperature 293K
Resolution 2.71 Å R-free 0.263
4RXN CRYSTALLOGRAPHIC REFINEMENT OF RUBREDOXIN AT 1.2 ANGSTROMS RESOLUTION Deposited 1984-10-15 Different construct 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 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.20 Å
4XNV The human P2Y1 receptor in complex with BPTU Deposited 2015-01-16 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 1–54（54 aa）
Mutation：D320N BUR 1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea × 1 CLR CHOLESTEROL × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 1PE PENTAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG2000MME Sodium Citrate
Resolution 2.20 Å R-free 0.230
4XNW The human P2Y1 receptor in complex with MRS2500 Deposited 2015-01-16 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 1–54（54 aa）
Mutation：D320N 2ID [(1R,2S,4S,5S)-4-[2-iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG400 Sodium citrate HEPES
Resolution 2.70 Å R-free 0.267
4XNW The human P2Y1 receptor in complex with MRS2500 Deposited 2015-01-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–54（54 aa）
Mutation：D320N 2ID [(1R,2S,4S,5S)-4-[2-iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG400 Sodium citrate HEPES
Resolution 2.70 Å R-free 0.267
5RXN COMBINED CRYSTALLOGRAPHIC REFINEMENT AND ENERGY MINIMIZATION OF RUBREDOXIN AT 1.2 ANGSTROM RESOLUTION Deposited 1984-10-15 Different construct 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 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.20 Å
5UIW Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV entry inhibitor 5P7-CCL5 Deposited 2017-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–54（54 aa）
Mutation：C58Y, G163N, A233D, K303E ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 OLA OLEIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.3；295.5 K；29% (v/v) PEG 400, 120 mM lithium citrate, 1.2% (w/v) 1,5-Diaminopentane dihydrochloride, 100 mM 2-(N-morpholino)ethanesulfonic acid
Resolution 2.20 Å R-free 0.250
5VBL Structure of apelin receptor in complex with agonist peptide Deposited 2017-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–54（54 aa） Fragment：UNP residues 7-229, UNP residues 1-54, UNP residues 243-330
Mutation：V117A, T177N,W261K, C325L, C326M ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM MES pH 6.1, 26% PEG500 DME, 125mM MgCl2, 100mM NaCl, 500uM AMG3054
Resolution 2.60 Å R-free 0.256
6AKX The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21 Deposited 2018-09-04 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 1–54（54 aa）
Mutation：C58Y, G163N, A233D, K303E ZN ZINC ION × 1 NO3 NITRATE ION × 1 A4R N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-2-yl)propyl]cyclopentanecarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；PEG 400, HEPES pH 7.5, ammonium acetate
Resolution 2.80 Å R-free 0.269
6AKX The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21 Deposited 2018-09-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–54（54 aa）
Mutation：C58Y, G163N, A233D, K303E ZN ZINC ION × 1 NO3 NITRATE ION × 1 A4R N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-2-yl)propyl]cyclopentanecarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；PEG 400, HEPES pH 7.5, ammonium acetate
Resolution 2.80 Å R-free 0.269
6AKY The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34 Deposited 2018-09-04 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 1–54（54 aa）
Mutation：C58Y, G163N, A233D, K303E ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 A4X 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-3-yl)propyl]cyclohexane-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG400, HEPES, ammonium acetate
Resolution 2.80 Å R-free 0.283
6BD4 Crystal structure of human apo-Frizzled4 receptor Deposited 2017-10-21 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 1–54（54 aa）
Mutation：M309L, C450I, C507F, S508Y ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 OLA OLEIC ACID × 5 SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium cacodylate trihydrate (pH 6.0), 80 mM Magnesium Sulfate, 30% PEG400, 1.5-2.5% v/v (+/-)-2-Methyl-2,4-pentanediol
Resolution 2.40 Å R-free 0.233
6GPS CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812 Deposited 2018-06-07 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 1–54（54 aa） Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ;
Mutation：;N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E ; ZN ZINC ION × 1 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；reconstituted into lipidic cubic phase (LCP) by mixing with 9.9 MAG (Monoolein, Sigma) using a syringe mixer as described previously (Caffrey and Cherezov, 2009). 35 % (w/w) of the receptor solution was mixed with 61.5 % monoolein (w/w), additionally supplemented with 3.5 % cholesterol (w/w). Crystallization trials were performed in 96-well glass sandwich plates (Molecular Dimensions). The LCP drops were pipetted in a bolus volume of 50 nl using a gryphon robot and overlaid with 800 nl of precipitant solution per well. Diffracting quality crystals were obtained with 0.1 M MES pH 6.0, 0.2 M ammonium acetate and 40 % PEG400
Resolution 3.30 Å R-free 0.296
6IIU Crystal structure of the human thromboxane A2 receptor bound to ramatroban Deposited 2018-10-07 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 1–54（54 aa）
Mutation：M1007W/H1102I/R1106L/L247A A8X 3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propanoic acid × 1 ZN ZINC ION × 1 CLR CHOLESTEROL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；Magnesium acetate, PEG 500 DME
Resolution 2.50 Å R-free 0.218
6IIV Crystal structure of the human thromboxane A2 receptor bound to daltroban Deposited 2018-10-07 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 1–54（54 aa）
Mutation：M1007W/H1102I/R1106L/L247A A90 2-[4-[2-[(4-chlorophenyl)sulfonylamino]ethyl]phenyl]ethanoic acid × 1 ZN ZINC ION × 1 CLR CHOLESTEROL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；Magnesium acetate, PEG 400
Resolution 3.00 Å R-free 0.237
6KNM Apelin receptor in complex with single domain antibody Deposited 2019-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–54（54 aa）
Mutation：V117A, T177N,W261K, C325L, C326M,V117A, T177N,W261K, C325L, C326M,V117A, T177N,W261K, C325L, C326M ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES pH 6.1, 26% PEG500 DME, 125 mM MgCl2, 100 mM NaCl
Resolution 3.20 Å R-free 0.305
6LI2 Crystal structure of GPR52 ligand free form with rubredoxin 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 2–54（53 aa）
Mutation：W278Q, C314P, S318A, N321D, V323T ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 11 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；0.08-0.1 M magnesium sulphate, 0.1 M sodium cacodylate trihydrate pH 6.2, and 28-31% PEG300
Resolution 2.80 Å R-free 0.263
6LN2 Crystal structure of full length human GLP1 receptor in complex with Fab fragment (Fab7F38) Deposited 2019-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–54（54 aa）
Mutation：S193C,I196F,S225A,M233C,S271A,I317C,G318I,K346A,C347F,G361C,E387D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 97Y N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；200-300 mM Ammonium formate, 36% PEG 400, 5%-10% (w/v) Guanidine hydrochloride
Resolution 3.20 Å R-free 0.262
6ME6 XFEL crystal structure of human melatonin receptor MT2 in complex with 2-phenylmelatonin Deposited 2018-09-05 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 1–53（53 aa）
Chain B 1–53（53 aa）
Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 2 ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Resolution 2.80 Å R-free 0.249
6ME7 XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin Deposited 2018-09-05 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 1–53（53 aa）
Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Resolution 3.20 Å R-free 0.250
6ME7 XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin Deposited 2018-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–53（53 aa）
Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Resolution 3.20 Å R-free 0.250
6ME8 XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin Deposited 2018-09-05 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 1–53（53 aa）
Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Resolution 3.10 Å R-free 0.262
6ME8 XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin Deposited 2018-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–53（53 aa）
Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Resolution 3.10 Å R-free 0.262
6ME9 XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon Deposited 2018-09-05 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 1–53（53 aa）
Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Resolution 3.30 Å R-free 0.270
6ME9 XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon Deposited 2018-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–53（53 aa）
Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Resolution 3.30 Å R-free 0.270
7F1T Crystal structure of the human chemokine receptor CCR5 in complex with MIP-1a Deposited 2021-06-09 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 1–54（54 aa）
Mutation：T15C,T108C,C150Y,M156A,G255N,A376D,R417A,T427A,K446E ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM HEPES, pH 6.0, 250mM ammonium sulfate, 30% (v/v) PEG 400, 8% (v/v) PPG 400
Resolution 2.60 Å R-free 0.271
7SUS Crystal structure of Apelin receptor in complex with small molecule Deposited 2021-11-18 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 1–54（54 aa）
Mutation：V117A,E174C,T177N,M217C,I250C,C325L,C326M ZN ZINC ION × 1 8EH (1R,2S)-N-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-propane-2-sulfonamide × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES pH 6.1, 26% PEG500 DME, 125 mM MgCl2, 100 mM NaCl
Resolution 2.70 Å R-free 0.274

44 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RUBR_CLOPA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 204–257； UniProt 1–54 Author chain B； PDBConstruct 204–257； UniProt 1–54

C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2

Homo sapiens

UniProt P41597

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 29–231 Chain A； UniProt 235–321 Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ; ZN ZINC ION × 1 OLA OLEIC ACID × 11 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1 X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 6.5；293 K；protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using the IMISX in-situ crystallization plate. 40nl of LCP bolus were dispensed using the Mosquito LCP robot (TTP Labtech) and overlaid with 800 nl of precipitant solution. Crystals were obtained in 0.1 M bis-tris propane pH 6.5, 0.2 M potassium nitrate, 39% (v/v) PEG400, 3% (v/v) 1,2-propanediol Resolution 2.70 Å R-free 0.243
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 29–231 Chain B； UniProt 235–321 Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ; OLA OLEIC ACID × 3 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1 X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 6.5；293 K；protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using the IMISX in-situ crystallization plate. 40nl of LCP bolus were dispensed using the Mosquito LCP robot (TTP Labtech) and overlaid with 800 nl of precipitant solution. Crystals were obtained in 0.1 M bis-tris propane pH 6.5, 0.2 M potassium nitrate, 39% (v/v) PEG400, 3% (v/v) 1,2-propanediol Resolution 2.70 Å R-free 0.243

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 6GPX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5T1A Structure of CC Chemokine Receptor 2 with Orthosteric and Allosteric Antagonists Deposited 2016-08-18 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 2–233（232 aa） Fragment：UNP P41597-2 residues 2-328 with UNP P00720 residues 2-161 inserted after residues 233
Chain A 234–328（95 aa） Fragment：UNP P41597-2 residues 2-328 with UNP P00720 residues 2-161 inserted after residues 233
Mutation：L226S, K227R, T228A, L229S, L230K, R231S, C232R, R233I, N234P, E235P, K236S, K237R, R238E, H238K, R239K, C1054T, C1097A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L226S, K227R, T228A, L229S, L230K, R231S, C232R, R233I, N234P, E235P, K236S, K237R, R238E, H238K, R239K, C1054T, C1097A Non-standard monomer：Yes (specific site not provided by mmCIF) 73R (3S)-1-{(1S,2R,4R)-4-[methyl(propan-2-yl)amino]-2-propylcyclohexyl}-3-{[6-(trifluoromethyl)quinazolin-4-yl]amino}pyrrolidin-2-one × 1 VT5 (2~{R})-1-(4-chloranyl-2-fluoranyl-phenyl)-2-cyclohexyl-3-ethanoyl-4-oxidanyl-2~{H}-pyrrol-5-one × 1 SO4 SULFATE ION × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.1；295 K；Lipidic cubic phase made of monoolein and cholesterol, 100 mM 2-(N-morpholino)ethanesulfonic acid, pH 6.5, 30-32% (v/v) PEG 400, 75-85 mM lithium sulfate
Resolution 2.81 Å R-free 0.274
6GPS CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812 Deposited 2018-06-07 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 2–231（230 aa） Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ;
Chain A 235–374（140 aa） Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ;
Mutation：;N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E ; Mutation：;N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E ; ZN ZINC ION × 1 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；reconstituted into lipidic cubic phase (LCP) by mixing with 9.9 MAG (Monoolein, Sigma) using a syringe mixer as described previously (Caffrey and Cherezov, 2009). 35 % (w/w) of the receptor solution was mixed with 61.5 % monoolein (w/w), additionally supplemented with 3.5 % cholesterol (w/w). Crystallization trials were performed in 96-well glass sandwich plates (Molecular Dimensions). The LCP drops were pipetted in a bolus volume of 50 nl using a gryphon robot and overlaid with 800 nl of precipitant solution per well. Diffracting quality crystals were obtained with 0.1 M MES pH 6.0, 0.2 M ammonium acetate and 40 % PEG400
Resolution 3.30 Å R-free 0.296
7P8X Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a doubly sulfated CCR2 N-terminal peptide Deposited 2021-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 25–29（5 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) IMD IMIDAZOLE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.40 Å R-free 0.198
7XA3 Cryo-EM structure of the CCL2 bound CCR2-Gi complex Deposited 2022-03-17 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 × 6 PDB declaration: hexameric
Chain R 1–360（360 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCR2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–203； UniProt 29–231 Author chain A； PDBConstruct 258–344； UniProt 235–321 Author chain B； PDBConstruct 1–203； UniProt 29–231 Author chain B； PDBConstruct 258–344； UniProt 235–321

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6gpx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6gpx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6gpx
Deposition date deposition_date2018-06-07
Structure title titleCRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812
Keywords keywordsGPCR, Signalling, Drug-design, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.37 Å
Radius of gyration Rg (electron density) rg_electron27.72 Å
Forward intensity I(0) i058890400.00
Molecular weight molecular_weight70466.0 kDa
Excluded volume excluded_volume92528 ų
Envelope volume envelope_volume111410 ų
Hydration-shell volume shell_volume33395 ų
Envelope diameter envelope_diameter98.3 Å
Shell Rg shell_rg35.01 Å
Envelope Rg envelope_rg27.89 Å
Shape Rg shape_rg27.68 Å
Total Rg total_rg28.69 Å
Total atoms total_atoms10145
Residues n_residues587
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.5 Å
Rg (real space) rg_real29.33 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real5.8890e+07
I(0) uncertainty (real space) i0_real_error8.7510e+05
Rg (reciprocal space) rg_reciprocal29.35 Å
I(0) (reciprocal space) i0_reciprocal58890000.0000
Solution quality estimate total_estimate0.9067
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.4 Å
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8776000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.936
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6gpxB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
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8. Citations (1)

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9. Files and Curves (10)