5obh

Crystal structure of glycine binding protein in complex with bicuculline

Method: X-RAY DIFFRACTION Dmax: 99.0 Å Quality: GOOD

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

Soluble acetylcholine receptor

Aplysia californica

UniProt Q8WSF8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–236 Chain B; UniProt 1–236 Chain C; UniProt 1–236 Chain D; UniProt 1–236 Chain E; UniProt 1–236 Mutation:T53F, Q74R, Y110A, I135S, G162E, S206K, C207G, C208T, P209G ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 J94 (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium × 5 CL CHLORIDE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;Reservoir buffer: 0.2 M ammonium formate, 20 % PEG 3350 Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5. 2 mM bicuculline Resolution 2.40 Å R-free 0.249

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.

85 other PDB entries and 120 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8WSF8_APLCA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–236; UniProt 1–236 Author chain B; PDBConstruct 1–236; UniProt 1–236 Author chain C; PDBConstruct 1–236; UniProt 1–236 Author chain D; PDBConstruct 1–236; UniProt 1–236 Author chain E; PDBConstruct 1–236; UniProt 1–236

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 5obh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5obh
Deposition date deposition_date2017-06-27
Structure title titleCrystal structure of glycine binding protein in complex with bicuculline
Keywords keywordsreceptor, acetylcholine binding, 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_guinier31.98
Radius of gyration Rg (electron density) rg_electron30.33
Forward intensity I(0) i0229646000.00
Molecular weight molecular_weight119330.0 kDa
Excluded volume excluded_volume148690 ų
Envelope volume envelope_volume193340 ų
Hydration-shell volume shell_volume50411 ų
Envelope diameter envelope_diameter106.0
Shell Rg shell_rg39.64
Envelope Rg envelope_rg29.69
Shape Rg shape_rg30.32
Total Rg total_rg31.21
Total atoms total_atoms8407
Residues n_residues1025
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 dmax99.0
Rg (real space) rg_real31.64
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real2.2960e+08
I(0) uncertainty (real space) i0_real_error3.3420e+06
Rg (reciprocal space) rg_reciprocal31.79
I(0) (reciprocal space) i0_reciprocal229700000.0000
Solution quality estimate total_estimate0.8818
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.5
Skewness Skewness skewness-0.070
Kurtosis Kurtosis kurtosis-0.556
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58190000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 1.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd5obha_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.0 — automated matches
Domain ID domain_idd5obhb_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.0 — automated matches
Domain ID domain_idd5obhc_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.0 — automated matches
Domain ID domain_idd5obhd_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.0 — automated matches
Domain ID domain_idd5obhe_
Class classb — All beta proteins
Fold Fold foldb.96 — Nicotinic receptor ligand binding domain-like
Superfamily Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
Family Family familyb.96.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id5obhA00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5obhB00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5obhC00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5obhD00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5obhE00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain

8. Citations (1)

9. Files and Curves (10)