4phu

Crystal structure of Human GPR40 bound to allosteric agonist TAK-875

Method: X-RAY DIFFRACTION Dmax: 106.4 Å Quality: GOOD

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

Free fatty acid receptor 1,Lysozyme

Homo sapiens

UniProt O14842

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 1–211 Chain A; UniProt 214–300 Fragment:UNP O14842 residues 2-213, UNP P00720 residues 2-161, UNP O14842 residues 214-300 Mutation:L42A,F88A,G103A,Y202F,S211G,G212S,C1154T,C1197A 2YB [(3S)-6-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy]biphenyl-3-yl}methoxy)-2,3-dihydro-1-benzofuran-3-yl]acetic acid × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 5 1PE PENTAETHYLENE GLYCOL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 8;294 K;29-31% Peg 400,100 mM Tris pH 8.0. 0.2 M Na Malonate,200 uM TAK-875 X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.2;294 K;39.8 % Peg 400, 100 mM Bis-Tris-Propane pH 7.2, 0.1 Ammonium Phosphate (monobasic), 200 uM TAK-875 Resolution 2.33 Å R-free 0.233

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.

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FFAR1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 14–224; UniProt 1–211 Author chain A; PDBConstruct 389–475; UniProt 214–300

Free fatty acid receptor 1,Lysozyme

Homo sapiens

UniProt P00720

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 2–161 Fragment:UNP O14842 residues 2-213, UNP P00720 residues 2-161, UNP O14842 residues 214-300 Mutation:L42A,F88A,G103A,Y202F,S211G,G212S,C1154T,C1197A 2YB [(3S)-6-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy]biphenyl-3-yl}methoxy)-2,3-dihydro-1-benzofuran-3-yl]acetic acid × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 5 1PE PENTAETHYLENE GLYCOL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 8;294 K;29-31% Peg 400,100 mM Tris pH 8.0. 0.2 M Na Malonate,200 uM TAK-875 X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.2;294 K;39.8 % Peg 400, 100 mM Bis-Tris-Propane pH 7.2, 0.1 Ammonium Phosphate (monobasic), 200 uM TAK-875 Resolution 2.33 Å R-free 0.233

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.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 227–386; UniProt 2–161

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 4phu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4phu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4phu
Deposition date deposition_date2014-05-07
Structure title titleCrystal structure of Human GPR40 bound to allosteric agonist TAK-875
Keywords keywords;GPR40, fatty acid binding protein, class A, g-protein coupled receptor, type II diabetes, TAK-875, fasiglifam, Fatty acid binding protein-Hydrolase complex ;; Fatty acid binding protein/Hydrolase
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.32
Radius of gyration Rg (electron density) rg_electron31.04
Forward intensity I(0) i032579400.00
Molecular weight molecular_weight48163.0 kDa
Excluded volume excluded_volume61885 ų
Envelope volume envelope_volume79294 ų
Hydration-shell volume shell_volume23305 ų
Envelope diameter envelope_diameter112.5
Shell Rg shell_rg34.82
Envelope Rg envelope_rg31.16
Shape Rg shape_rg31.03
Total Rg total_rg31.46
Total atoms total_atoms3399
Residues n_residues434
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax106.4
Rg (real space) rg_real31.77
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real3.2580e+07
I(0) uncertainty (real space) i0_real_error5.7390e+05
Rg (reciprocal space) rg_reciprocal31.58
I(0) (reciprocal space) i0_reciprocal32570000.0000
Solution quality estimate total_estimate0.7655
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.0
Skewness Skewness skewness0.499
Kurtosis Kurtosis kurtosis-0.601
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4800000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.607; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.278; Smooth: 0.847

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4phuA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)