4DKL: Mu-opioid receptor

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist. Determined by X-ray diffraction at 2.8 Å resolution. Released 21 Mar 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Mus musculus, Enterobacteria phage T4
Chains: 1
Atoms: 3,690
Mol. weight: 55.76 kDa
Ligands: BF0, CLR, MPG
Released: 21 Mar 2012

Explore 4DKL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DKL contains 23 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: 23 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	66-95	30
α-helix	102-130	29
α-helix	138-170	33
α-helix	172-178	7
α-helix	181-204	24
β-strand	206	1	1
α-helix	208	1
β-strand	209-211	3	2
β-strand	214-216	3	2
β-strand	219	1	1
α-helix	225-237	13
α-helix	238-242	5
α-helix	243-258	16
α-helix	1003-1011	9
β-strand	1014-1015	2	3
β-strand	1016	1	4
β-strand	1017-1019	3	3
β-strand	1025-1028	4	3
β-strand	1031-1034	4	3
α-helix	1040-1050	11
β-strand	1057	1	4
α-helix	1060-1079	20
α-helix	1084-1089	6
α-helix	1093-1106	14
α-helix	1108-1112	5
α-helix	1115-1122	8
α-helix	1126-1133	8
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	271-272	2
α-helix	273-305	33
α-helix	312-339	28
α-helix	341-351	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mu-type opioid receptor, lysozyme chimera	A	protein	464	Mus musculus, Enterobacteria phage T4	P00720, P42866 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DKL_1 Mu-type opioid receptor, lysozyme chimera (chains A)
GSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLA
LADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCH
PVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENL
LKICVFIFAFIMPVLIITVCYGLMILRLKSVRNIFEMLRIDEGLRLKIYKNTEGYYTIGI
GHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYD
SLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV
ITTFRTGTWDAYEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALITIPETTFQTVS
WHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSTIEQP

Ligands and cofactors

ID	Name	Formula	Copies
BF0	methyl 4-{[(5beta,6alpha)-17-(cyclopropylmethyl)-3,14-dihydroxy-4,5-epoxymorphi…	C25 H32 N2 O6	1
CLR	Cholesterol	C27 H46 O	1
MPG	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate	C21 H40 O4	2

Water and common crystallization additives (SO4, 1PE, CL) are not listed.

Primary citation

Crystal structure of the {mu}-opioid receptor bound to a morphinan antagonist. Manglik, A., Kruse, A.C., Kobilka, T.S. et al. Nature (2012) 485:321-326. DOI 10.1038/nature10954 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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