7e5e

Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20

Method: X-RAY DIFFRACTION Dmax: 120.8 Å Quality: GOOD

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

Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Homo sapiens

UniProt P63092

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 35–380 Not recorded GD20 × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.2;293 K;0.1M Tris 8.2, 26% PEG 4000, 0.8M LiCl Resolution 1.95 Å R-free 0.258
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 35–380 Not recorded GD20 × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.2;293 K;0.1M Tris 8.2, 26% PEG 4000, 0.8M LiCl Resolution 1.95 Å R-free 0.258
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 35–380 Not recorded GD20 × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.2;293 K;0.1M Tris 8.2, 26% PEG 4000, 0.8M LiCl Resolution 1.95 Å R-free 0.258
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 35–380 Not recorded GD20 × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.2;293 K;0.1M Tris 8.2, 26% PEG 4000, 0.8M LiCl Resolution 1.95 Å R-free 0.258

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.

348 other PDB entries and 353 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_HUMAN
Isoform P63092-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–348; UniProt 35–380 Author chain B; PDBConstruct 3–348; UniProt 35–380 Author chain C; PDBConstruct 3–348; UniProt 35–380 Author chain D; PDBConstruct 3–348; UniProt 35–380

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 7e5e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7e5e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7e5e
Deposition date deposition_date2021-02-18
Structure title titleCrystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
Keywords keywordsG protein, GNAS, adenylyl cyclase, inactive state, inhibitor, mRNA display, RaPID, cyclic peptide, GD20, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.44
Radius of gyration Rg (electron density) rg_electron36.86
Forward intensity I(0) i0404144000.00
Molecular weight molecular_weight162090.0 kDa
Excluded volume excluded_volume202330 ų
Envelope volume envelope_volume263250 ų
Hydration-shell volume shell_volume58742 ų
Envelope diameter envelope_diameter132.0
Shell Rg shell_rg43.69
Envelope Rg envelope_rg36.23
Shape Rg shape_rg36.89
Total Rg total_rg37.20
Total atoms total_atoms11411
Residues n_residues1367
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 dmax120.8
Rg (real space) rg_real37.32
Rg uncertainty (real space) rg_real_error1.04
I(0) (real space) i0_real4.0410e+08
I(0) uncertainty (real space) i0_real_error6.5680e+06
Rg (reciprocal space) rg_reciprocal37.40
I(0) (reciprocal space) i0_reciprocal404200000.0000
Solution quality estimate total_estimate0.8889
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.0
Skewness Skewness skewness0.258
Kurtosis Kurtosis kurtosis-0.370
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85000000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.846

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7e5eA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology400 — GI Alpha 1, domain 2-like
Homologous superfamily homologous superfamily10 — GI Alpha 1, domain 2-like
Domain ID domain_id7e5eB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology400 — GI Alpha 1, domain 2-like
Homologous superfamily homologous superfamily10 — GI Alpha 1, domain 2-like
Domain ID domain_id7e5eC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology400 — GI Alpha 1, domain 2-like
Homologous superfamily homologous superfamily10 — GI Alpha 1, domain 2-like
Domain ID domain_id7e5eD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology400 — GI Alpha 1, domain 2-like
Homologous superfamily homologous superfamily10 — GI Alpha 1, domain 2-like

8. Citations (1)

9. Files and Curves (10)