6ME5: PDB entry 6ME5

XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine. Determined by X-ray diffraction at 3.2 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Pyrococcus abyssi GE5
Chains: 1
Atoms: 3,695
Mol. weight: 57.12 kDa
Ligands: OLA, AWY
Released: 24 Apr 2019

Explore 6ME5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ME5 contains 25 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	24-54	31
α-helix	61-63	3
α-helix	64-78	15
α-helix	80-90	11
α-helix	98-134	37
α-helix	144-159	16
α-helix	161-165	5
β-strand	168-171	4	1
α-helix	172-174	3
β-strand	176-179	4	1
α-helix	185-192	8
α-helix	193-197	5
α-helix	198-1001	22
α-helix	1009-1011	3
α-helix	1016-1026	11
β-strand	1033-1038	6	2
β-strand	1041	1	3
α-helix	1048-1059	12
α-helix	1062-1066	5
β-strand	1067-1072	6	2
β-strand	1075	1	3
α-helix	1077-1089	13
β-strand	1093-1096	4	2
α-helix	1102-1111	10
β-strand	1114-1117	4	2
α-helix	1126-1132	7
β-strand	1137-1141	5	2
α-helix	1146-1149	4
β-strand	1156-1158	3	2
α-helix	1163-1174	12
α-helix	1178-228	20
α-helix	235-263	29
α-helix	265-271	7
α-helix	274-298	25
α-helix	300-314	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase	A	protein	503	Homo sapiens, Pyrococcus abyssi GE5	P48039 (AlphaFold model), Q9V2J8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6ME5_1 chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase (chains A)
GTSQPVLRGDGARPSWLASALACVLIFTIVVDILGNLLVILSVYRNKKLRNAGNIFVVSL
AVANLVVAIYPYPLVLMSIFNNGWNFGYLHCQVSAFLMGLSVIGSIWNITGIAIDRYLYI
CHSLKYDKLYSSKNSLCYVLLIWLLTLAAVLPNLRAGTLQYDPRIYSCTFAQSVSSAYTI
AVVVFHFLVPMIIVIFCYLRIWILVLQVRGIDCSFWNESYLTGSRDERKKSLLSKFGMDE
GVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHG
NVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIIT
NETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSKLKPQDFRNFVTMFV
VFVLFAICFAPLNFIGLAVASDPASMVPRIPEWLFVASYYMAYFNSCLNPIIYGLLDQNF
RKEYRRIIVSLCTARVFFVDSSN

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	1
AWY	~{N}-[2-(7-methoxynaphthalen-1-yl)ethyl]ethanamide	C15 H17 N O2	1

Primary citation

Structural basis of ligand recognition at the human MT1melatonin receptor. Stauch, B., Johansson, L.C., McCorvy, J.D. et al. Nature (2019) 569:284-288. DOI 10.1038/s41586-019-1141-3 · PubMed

Other PDB entries of the same protein (UniProt P48039 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ME2 2.8 Å, XFEL crystal structure of human melatonin receptor MT1 in complex with ramelteon
6ME3 2.9 Å, XFEL crystal structure of human melatonin receptor MT1 in complex with 2-phenylmelatonin
7VGY 3.1 Å, Melatonin receptor1-2-Iodomelatonin-Gicomplex
6ME4 3.2 Å, XFEL crystal structure of human melatonin receptor MT1 in complex with 2-iodomelatonin
6PS8 3.3 Å, XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin.
7DB6 3.3 Å, human melatonin receptor MT1 - Gi1 complex
7VGZ 3.3 Å, MT1-remalteon-Gi complex

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