SAXSdb — 8wkz

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

Melanocortin receptor 4

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 16–222 Chain A； UniProt 236–320	Non-standard monomer：Yes (specific site not provided by mmCIF)	;[N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}propyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](azido)(hydroxy)copper ; × 1 CA CALCIUM ION × 1 OLA OLEIC ACID × 5	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；PEG 400, Bis-tris propane buffer, CaCl2-2H2O	Resolution 3.30 Å R-free 0.272

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.

Other PDB	Difference from Current Entry 8WKZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6W25 Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with SHU9119 Deposited 2020-03-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 16–222（207 aa） Chain A 236–320（85 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 OLA OLEIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.9；293 K；19% PEG 400, 100 mM Bis-tris propane buffer, and 50 mM CaCl2 2H2O	Resolution 2.75 Å R-free 0.259
7AUE Melanocortin receptor 4 (MC4R) Gs protein complex Deposited 2020-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–332（332 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
7F53 Cryo-EM structure of a-MSH-MC4R-Gs_Nb35 complex Deposited 2021-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–332（332 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7F54 Cryo-EM structure of afamelanotide-MC4R-Gs_Nb35 complex Deposited 2021-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–332（332 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7F55 Cryo-EM structure of bremelanotide-MC4R-Gs_Nb35 complex Deposited 2021-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–332（332 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7F58 Cryo-EM structure of THIQ-MC4R-Gs_Nb35 complex Deposited 2021-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–332（332 aa）	Not recorded	1I8 (3R)-N-[(2R)-3-(4-chlorophenyl)-1-[4-cyclohexyl-4-(1,2,4-triazol-1-ylmethyl)piperidin-1-yl]-1-oxidanylidene-propan-2-yl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7PIU Cryo-EM structure of the agonist setmelanotide bound to the active melanocortin-4 receptor (MC4R) in complex with the heterotrimeric Gs protein at 2.6 A resolution. Deposited 2021-08-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–332（332 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å
7PIV Active Melanocortin-4 receptor (MC4R)- Gs protein complex bound to agonist NDP-alpha-MSH at 2.86 A resolution. Deposited 2021-08-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–332（332 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
8QJ2 Structure of active state MC4R in complex with a potent ligand mimicking nanobody Deposited 2023-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–332（332 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8WKY Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with S25 Deposited 2023-09-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 16–222（207 aa） Chain A 236–320（85 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 OLA OLEIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG 400, Bis-tris propane buffer, CaCl2-2H2O	Resolution 2.90 Å R-free 0.267
9K3K Cryo-EM structure of the unliganded human melanocortin receptor 4 (MC4R)-Gs complex Deposited 2024-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–332（332 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MC4R_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 28–234； UniProt 16–222 Author chain A； PDBConstruct 431–515； UniProt 236–320

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	8wkz
Deposition date deposition_date	2023-09-28
最后修订 last_revision	2024-08-07
Structure title title	Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with S31
Keywords keywords	Ca++ cofactor, GPCR, PGS fusion, membrane protein, LCP; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.38 Å
Radius of gyration Rg (electron density) rg_electron	29.81 Å
Forward intensity I(0) i0	39939300.00
Molecular weight molecular_weight	53686.0 kDa
Excluded volume excluded_volume	69041 Å³
Envelope volume envelope_volume	84533 Å³
Hydration-shell volume shell_volume	25539 Å³
Envelope diameter envelope_diameter	106.1 Å
Shell Rg shell_rg	34.35 Å
Envelope Rg envelope_rg	29.90 Å
Shape Rg shape_rg	29.84 Å
Total Rg total_rg	30.17 Å
Total atoms total_atoms	3767
Residues n_residues	472
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	101.8 Å
Rg (real space) rg_real	30.66 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	3.9940e+07
I(0) uncertainty (real space) i0_real_error	7.2540e+05
Rg (reciprocal space) rg_reciprocal	30.55 Å
I(0) (reciprocal space) i0_reciprocal	39940000.0000
Solution quality estimate total_estimate	0.8233
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	8007000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.626; Smooth: 0.923

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Melanocortin receptor 4
Molecular weight formula_weight	60197.3 kDa
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	3769

MKTIIALSYIFCLVFADYKDDDDAGRAWNRSSYRLHSNASESLGKGYSDGGCYEQLFVSPVVFVTLGVISLLENILVIVAIAKNKNLHSPMYFFICSLAVADMLVSVSLGFETIVITLLNSTDTDAQSFTVNIDNVIDSVICASLLASICSLLSIAVDRYFTIFYALQYHNIMTVKRVGIIISCIWAACTVSGILFIIYSDSSAVIICLITMFFTMLALMASLYVHMFLMARLHGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSRQGANMKGAITLTILIGVFVVCWAPFFLHLIFYISCPQNPYCVCFMSHFNLYLILIMCNSIINPLIYALRSQELRKTFKEIICCYEFLEVLFQGPHHHHHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	;[N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}propyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](azido)(hydroxy)copper ;
Molecular weight formula_weight	1194.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XLDPXRWRKX

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	OLEIC ACID
Molecular weight formula_weight	282.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	167.460 Å
Unit-cell length b length_b	44.940 Å
Unit-cell length c length_c	89.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.60 °
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	3.300 Å
Low-resolution limit resolution_low	44.390 Å
R factor r_factor	0.2159
R_work r_work	0.2132
R_free r_free	0.2718

fit	/app/data/saxs_computation/wk/8wkz/8wkz.fit
pddf	/app/data/pr_computation/wk/8wkz/8wkz.pr.out
profile	/app/data/saxs_computation/wk/8wkz/8wkz.dat

Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with S31

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

Melanocortin receptor 4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)