5l4e

X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental

Method: X-RAY DIFFRACTION Dmax: 124.5 Å Quality: GOOD

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

Proton-gated ion channel

Gloeobacter

UniProt Q7NDN8

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 homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 43–359 Chain B; UniProt 43–359 Chain C; UniProt 43–359 Chain D; UniProt 43–359 Chain E; UniProt 43–359 Not recorded D12 DODECANE × 1 CL CHLORIDE ION × 5 EDP 5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;291 K;100 mM NaAcetate pH4 200 NaSCN 12-15% PEG4000 16% glycerol 3%DMSO Resolution 3.50 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.

129 other PDB entries and 135 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLIC_GLOVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–317; UniProt 43–359 Author chain B; PDBConstruct 1–317; UniProt 43–359 Author chain C; PDBConstruct 1–317; UniProt 43–359 Author chain D; PDBConstruct 1–317; UniProt 43–359 Author chain E; PDBConstruct 1–317; UniProt 43–359

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 5l4e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l4e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5l4e
Deposition date deposition_date2016-05-25
Structure title titleX-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental
Keywords keywordsmembrane protein, barbiturates, transport protein; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.03
Radius of gyration Rg (electron density) rg_electron37.35
Forward intensity I(0) i0404587000.00
Molecular weight molecular_weight178270.0 kDa
Excluded volume excluded_volume228800 ų
Envelope volume envelope_volume289630 ų
Hydration-shell volume shell_volume63648 ų
Envelope diameter envelope_diameter129.1
Shell Rg shell_rg44.56
Envelope Rg envelope_rg36.95
Shape Rg shape_rg37.33
Total Rg total_rg37.86
Total atoms total_atoms12633
Residues n_residues1555
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 dmax124.5
Rg (real space) rg_real37.95
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real4.0460e+08
I(0) uncertainty (real space) i0_real_error7.3830e+06
Rg (reciprocal space) rg_reciprocal38.00
I(0) (reciprocal space) i0_reciprocal404600000.0000
Solution quality estimate total_estimate0.8786
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.4
Skewness Skewness skewness0.331
Kurtosis Kurtosis kurtosis-0.288
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha90510000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.906

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id5l4eA01
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_id5l4eA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5l4eB01
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_id5l4eB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5l4eC01
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_id5l4eC02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5l4eD01
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_id5l4eD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5l4eE01
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_id5l4eE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain

8. Citations (1)

9. Files and Curves (10)