SAXSdb — 6me7

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

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZINC ION × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUBR_CLOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 308–360； UniProt 1–53 Author chain B； PDBConstruct 308–360； UniProt 1–53

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

Homo sapiens

UniProt P0ABE7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZINC ION × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C562_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–106； UniProt 23–128 Author chain B； PDBConstruct 1–106； UniProt 23–128

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

Homo sapiens

UniProt P49286

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZINC ION × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTR1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 111–307； UniProt 35–231 Author chain A； PDBConstruct 361–460； UniProt 241–340 Author chain B； PDBConstruct 111–307； UniProt 35–231 Author chain B； PDBConstruct 361–460； UniProt 241–340

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	6me7
Deposition date deposition_date	2018-09-05
Structure title title	XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin
Keywords keywords	;GPCR, melatonin receptor type 1B (MT2), H208A mutation, membrane protein, 2-phenylmelatonin, XFEL, LCP, BRIL, Rubredoxin, circadian rhythm, jetlag, type 2 diabetes ;; MEMBRANE PROTEIN
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.

6me7__assembly_1__model_1

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

Download this curve (.dat)

6me7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6me7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.64 Å
Rg (electron density)	28.58 Å
Total Rg	29.09 Å
Atom count	3367
Residues	448
Excluded volume	60508 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6me7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6me7__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
Molecular weight formula_weight	51447.5 kDa
Mutation mutation	M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6188

ADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGDGARPSWVAPALSAVLIVTTAVDVVGNLLVILSVLRNRKLRNAGNLFLVSLALANLVVAFYPYPLILVAIFYDGWAFGEEHCKASAFVMGLSVIGSVWNITAIAIDRYLYICHSMAYHRIYRRWHTPLHICLIWLLTVVALLPNFFVGSLEYDPRIYSCTFIQTASTQYTAAVVVIAFLLPIAVVSFCYLRIWVLVLQARMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVECLKPSDLRSFLTMFVVFVIFAICFAPLNCIGLAVAINPQEMAPQIPEGLFVTSYLLAYFNSCLNPIVYGLLDQNFRREYKRILLALWNPRHCIQDASKGS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide
Molecular weight formula_weight	308.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6me7A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	10 — Cytochrome c/b562

Domain ID domain_id	6me7B01
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

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Unit-cell length a length_a	69.230 Å
Unit-cell length b length_b	146.190 Å
Unit-cell length c length_c	77.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	21.990 Å
R factor r_factor	0.2260
R_work r_work	0.2240
R_free r_free	0.2500

XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin

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

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

State in the Current Structure

Other States of the Same Protein in the Database

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

State in the Current Structure

Other States of the Same Protein in the Database

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

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

6me7__assembly_1__model_1

6me7__assembly_1__model_1 | I(q)

6me7__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 (4)

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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin

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

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

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

6me7__assembly_1__model_1

6me7__assembly_1__model_1 | I(q)

6me7__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 (4)

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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)