5tzr

GPR40 in complex with partial agonist MK-8666

Method: X-RAY DIFFRACTION Dmax: 109.2 Å Quality: GOOD

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

Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1

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 Mutation:L42A, F88A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R NA SODIUM ION × 1 MK6 (5aR,6S,6aS)-3-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy][1,1'-biphenyl]-3-yl}methoxy)-5,5a,6,6a-tetrahydrocyclopropa[4,5]cyclopenta[1,2-c]pyridine-6-carboxylic acid × 1 MLI MALONATE ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.7;293 K;25-28%PEG 400, 0.2M sodium malonate, 0.1M Tris pH7.7 Resolution 2.20 Å R-free 0.228

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,Endolysin,Free fatty acid receptor 1

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 Mutation:L42A, F88A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R NA SODIUM ION × 1 MK6 (5aR,6S,6aS)-3-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy][1,1'-biphenyl]-3-yl}methoxy)-5,5a,6,6a-tetrahydrocyclopropa[4,5]cyclopenta[1,2-c]pyridine-6-carboxylic acid × 1 MLI MALONATE ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.7;293 K;25-28%PEG 400, 0.2M sodium malonate, 0.1M Tris pH7.7 Resolution 2.20 Å R-free 0.228

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 ENLYS_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 5tzr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tzr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tzr
Deposition date deposition_date2016-11-22
Structure title titleGPR40 in complex with partial agonist MK-8666
Keywords keywordsFFAR1, partial agonist, 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_guinier31.38
Radius of gyration Rg (electron density) rg_electron31.14
Forward intensity I(0) i032873300.00
Molecular weight molecular_weight49065.0 kDa
Excluded volume excluded_volume63304 ų
Envelope volume envelope_volume81234 ų
Hydration-shell volume shell_volume23789 ų
Envelope diameter envelope_diameter113.1
Shell Rg shell_rg35.01
Envelope Rg envelope_rg31.31
Shape Rg shape_rg31.12
Total Rg total_rg31.60
Total atoms total_atoms3464
Residues n_residues437
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 dmax109.2
Rg (real space) rg_real31.83
Rg uncertainty (real space) rg_real_error1.02
I(0) (real space) i0_real3.2870e+07
I(0) uncertainty (real space) i0_real_error5.6460e+05
Rg (reciprocal space) rg_reciprocal31.65
I(0) (reciprocal space) i0_reciprocal32870000.0000
Solution quality estimate total_estimate0.7668
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.8
Skewness Skewness skewness0.501
Kurtosis Kurtosis kurtosis-0.599
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5115000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.557; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.380; Smooth: 0.913

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id5tzrA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)