4dkl

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist

Method: X-RAY DIFFRACTION

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

Mu-type opioid receptor, lysozyme chimera

Enterobacteria phage T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	methyl 4-{[(5beta,6alpha)-17-(cyclopropylmethyl)-3,14-dihydroxy-4,5-epoxymorphinan-6-yl]amino}-4-oxobutanoate × 2 SULFATE ION × 24 CHOLESTEROL × 2 [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 4 PENTAETHYLENE GLYCOL × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYS_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 213–372； UniProt 2–161

Mu-type opioid receptor, lysozyme chimera

Enterobacteria phage T4

UniProt P42866

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	methyl 4-{[(5beta,6alpha)-17-(cyclopropylmethyl)-3,14-dihydroxy-4,5-epoxymorphinan-6-yl]amino}-4-oxobutanoate × 2 SULFATE ION × 24 CHOLESTEROL × 2 [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 4 PENTAETHYLENE GLYCOL × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OPRM_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–212； UniProt 52–263 Author chain A； PDBConstruct 373–463； UniProt 270–360

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4dkl
Deposition date deposition_date	2012-02-03
Structure title title	Crystal structure of the mu-opioid receptor bound to a morphinan antagonist
Keywords keywords	G-protein coupled receptor, 7 transmembrane receptor, SIGNALING PROTEIN-ANTAGONIST complex; SIGNALING PROTEIN/ANTAGONIST
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4dkl__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4dkl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dkl__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.56 Å
Rg (electron density)	32.41 Å
Total Rg	33.04 Å
Atom count	7306
Residues	884
Excluded volume	132900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dkl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Mu-type opioid receptor, lysozyme chimera
Molecular weight formula_weight	52778.9 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	D1020N, C1054T, C1097A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3690

GSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRNIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSTIEQP

Source Source

Source organism organism	Enterobacteria phage T4
Common name common_name	mouse, bacteriophage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	methyl 4-{[(5beta,6alpha)-17-(cyclopropylmethyl)-3,14-dihydroxy-4,5-epoxymorphinan-6-yl]amino}-4-oxobutanoate
Molecular weight formula_weight	456.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4dklA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

Domain ID domain_id	4dklA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	70.882 Å
Unit-cell length b length_b	174.730 Å
Unit-cell length c length_c	68.353 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.488 Å
R factor r_factor	0.2347
R_work r_work	0.2326
R_free r_free	0.2753

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist

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

Mu-type opioid receptor, lysozyme chimera

State in the Current Structure

Other States of the Same Protein in the Database

Mu-type opioid receptor, lysozyme chimera

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4dkl__assembly_1__model_1

4dkl__assembly_1__model_1 | I(q)

4dkl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist

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

Mu-type opioid receptor, lysozyme chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mu-type opioid receptor, lysozyme chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4dkl__assembly_1__model_1

4dkl__assembly_1__model_1 | I(q)

4dkl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)