4ej4

Structure of the delta opioid receptor bound to naltrindole

Method: X-RAY DIFFRACTION Dmax: 102.7 Å Quality: GOOD

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

Delta-type opioid receptor, Lysozyme chimera

Enterobacteria phage T4

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:P32300 residues 36-244, 251-342 Mutation:D1020N, C1054T, C1097A EJ4 (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;293 K;29-33% PEG 400, 100 mM HEPES pH 7.5, 120-180 mM sodium citrate, 350 mM Magnesium chloride. Protein was mixed 1:1.5 (w:w) with 91% monoolein 9% cholesterol mixture by weight, Lipidic cubic phase, temperature 293K Resolution 3.40 Å R-free 0.282

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 210–369; UniProt 2–161

Delta-type opioid receptor, Lysozyme chimera

Enterobacteria phage T4

UniProt P32300

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 36–244 Chain A; UniProt 251–342 Fragment:P32300 residues 36-244, 251-342 Mutation:D1020N, C1054T, C1097A EJ4 (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;293 K;29-33% PEG 400, 100 mM HEPES pH 7.5, 120-180 mM sodium citrate, 350 mM Magnesium chloride. Protein was mixed 1:1.5 (w:w) with 91% monoolein 9% cholesterol mixture by weight, Lipidic cubic phase, temperature 293K Resolution 3.40 Å R-free 0.282

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name OPRD_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–209; UniProt 36–244 Author chain A; PDBConstruct 370–461; UniProt 251–342

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 4ej4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ej4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ej4
Deposition date deposition_date2012-04-06
Structure title titleStructure of the delta opioid receptor bound to naltrindole
Keywords keywordsG-protein coupled receptor, 7 transmembrane receptor, opioid receptor, SIGNALING PROTEIN, Hydrolase-Antagonist complex; SIGNALING PROTEIN, Hydrolase/Antagonist
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.64
Radius of gyration Rg (electron density) rg_electron31.15
Forward intensity I(0) i033076000.00
Molecular weight molecular_weight48031.0 kDa
Excluded volume excluded_volume61418 ų
Envelope volume envelope_volume81446 ų
Hydration-shell volume shell_volume23476 ų
Envelope diameter envelope_diameter103.9
Shell Rg shell_rg35.48
Envelope Rg envelope_rg31.00
Shape Rg shape_rg31.17
Total Rg total_rg31.54
Total atoms total_atoms3382
Residues n_residues442
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 dmax102.7
Rg (real space) rg_real31.95
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real3.3080e+07
I(0) uncertainty (real space) i0_real_error4.9710e+05
Rg (reciprocal space) rg_reciprocal31.83
I(0) (reciprocal space) i0_reciprocal33070000.0000
Solution quality estimate total_estimate0.8129
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.376
Kurtosis Kurtosis kurtosis-0.794
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6086000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.718; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.605; Smooth: 0.804

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4ej4A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
Domain ID domain_id4ej4A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)