5dhg

The crystal structure of nociceptin/orphanin FQ peptide receptor (NOP) in complex with C-35 (PSI Community Target)

Method: X-RAY DIFFRACTION Dmax: 105.7 Å Quality: GOOD

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

Soluble cytochrome b562,Nociceptin receptor

Homo sapiens

UniProt P0ABE7

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 23–128 Mutation:M1007W, H1102I, R1106L DGV 1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide × 1 OLA OLEIC ACID × 3 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.5;293 K;25-35% (V/V) PEG400, 130-200 MM POTASSIM SODIUM TARTRATE TETRAHYDRATE, 100 MM BIS-TRIS PROPANE, PH 6.4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K Resolution 3.00 Å R-free 0.275
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 23–128 Mutation:M1007W, H1102I, R1106L DGV 1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide × 1 OLA OLEIC ACID × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.5;293 K;25-35% (V/V) PEG400, 130-200 MM POTASSIM SODIUM TARTRATE TETRAHYDRATE, 100 MM BIS-TRIS PROPANE, PH 6.4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K Resolution 3.00 Å R-free 0.275
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 23–128 Chain B; UniProt 23–128 Mutation:M1007W, H1102I, R1106L DGV 1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide × 2 OLA OLEIC ACID × 5 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.5;293 K;25-35% (V/V) PEG400, 130-200 MM POTASSIM SODIUM TARTRATE TETRAHYDRATE, 100 MM BIS-TRIS PROPANE, PH 6.4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K Resolution 3.00 Å R-free 0.275

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.

714 other PDB entries and 820 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 11–116; UniProt 23–128 Author chain B; PDBConstruct 11–116; UniProt 23–128

Soluble cytochrome b562,Nociceptin receptor

Homo sapiens

UniProt P41146

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 43–339 Mutation:M1007W, H1102I, R1106L DGV 1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide × 1 OLA OLEIC ACID × 3 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.5;293 K;25-35% (V/V) PEG400, 130-200 MM POTASSIM SODIUM TARTRATE TETRAHYDRATE, 100 MM BIS-TRIS PROPANE, PH 6.4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K Resolution 3.00 Å R-free 0.275
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 43–339 Mutation:M1007W, H1102I, R1106L DGV 1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide × 1 OLA OLEIC ACID × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.5;293 K;25-35% (V/V) PEG400, 130-200 MM POTASSIM SODIUM TARTRATE TETRAHYDRATE, 100 MM BIS-TRIS PROPANE, PH 6.4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K Resolution 3.00 Å R-free 0.275
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 43–339 Chain B; UniProt 43–339 Mutation:M1007W, H1102I, R1106L DGV 1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide × 2 OLA OLEIC ACID × 5 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 7.5;293 K;25-35% (V/V) PEG400, 130-200 MM POTASSIM SODIUM TARTRATE TETRAHYDRATE, 100 MM BIS-TRIS PROPANE, PH 6.4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K Resolution 3.00 Å R-free 0.275

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.

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OPRX_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 117–413; UniProt 43–339 Author chain B; PDBConstruct 117–413; UniProt 43–339

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 5dhg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5dhg
Deposition date deposition_date2015-08-30
Structure title titleThe crystal structure of nociceptin/orphanin FQ peptide receptor (NOP) in complex with C-35 (PSI Community Target)
Keywords keywords;Nociceptin/orphanin FQ peptide receptor, NOP, ORL-1, N/OFQ, opioid receptor, G protein-coupled receptor, GPCR, membrane protein, lipidic cubic phase, BRET, receptor-ligand conformational pair, Structural Genomics, PSI-Biology, GPCR Network, SIGNALING PROTEIN, PSICNT-127 ;; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.53
Radius of gyration Rg (electron density) rg_electron31.51
Forward intensity I(0) i070469500.00
Molecular weight molecular_weight72117.0 kDa
Excluded volume excluded_volume92868 ų
Envelope volume envelope_volume122570 ų
Hydration-shell volume shell_volume33192 ų
Envelope diameter envelope_diameter108.3
Shell Rg shell_rg37.21
Envelope Rg envelope_rg31.54
Shape Rg shape_rg31.50
Total Rg total_rg32.10
Total atoms total_atoms5071
Residues n_residues660
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 dmax105.7
Rg (real space) rg_real32.52
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real7.0470e+07
I(0) uncertainty (real space) i0_real_error1.1240e+06
Rg (reciprocal space) rg_reciprocal32.53
I(0) (reciprocal space) i0_reciprocal70470000.0000
Solution quality estimate total_estimate0.8901
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.3
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12800000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.839

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5dhga_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.13 — Class A G protein-coupled receptor (GPCR)-like
Superfamily Superfamily superfamilyf.13.1 — Class A G protein-coupled receptor (GPCR)-like
Family Family familyf.13.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id5dhgA00
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_id5dhgB02
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

8. Citations (1)

9. Files and Curves (10)