4DJH: Human kappa opioid receptor

Structure of the human kappa opioid receptor in complex with JDTic. Determined by X-ray diffraction at 2.9 Å resolution. Released 21 Mar 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo Sapiens, Enterobacteria phage T4
Chains: 2
Atoms: 7,089
Mol. weight: 110.63 kDa
Ligands: OLC, CIT, JDC
Released: 21 Mar 2012

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

Secondary structure: helices and β-sheets

4DJH contains 49 α-helices and 16 β-strands across 2 chains. 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	57-86	30
α-helix	88-90	3
α-helix	93-109	17
α-helix	112-121	10
α-helix	127-159	33
α-helix	170-196	27
β-strand	197-201	5	1
β-strand	208-212	5	1
α-helix	214	1
α-helix	219-231	13
α-helix	232-236	5
α-helix	237-259	23
α-helix	1003-1010	8
β-strand	1014-1015	2	2
β-strand	1016	1	3
β-strand	1017-1019	3	2
β-strand	1025-1028	4	2
β-strand	1031-1034	4	2
α-helix	1039-1050	12
β-strand	1057	1	3
α-helix	1060-1080	21
α-helix	1084-1090	7
α-helix	1093-1112	20
α-helix	1115-1122	8
α-helix	1126-1134	9
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	264-266	3
α-helix	267-299	33
α-helix	309-333	25
α-helix	335-345	11

Chain B: 26 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	57-86	30
α-helix	88-90	3
α-helix	93-109	17
α-helix	112-121	10
α-helix	127-161	35
α-helix	163-169	7
α-helix	172-196	25
β-strand	197-201	5	4
α-helix	202	1
β-strand	208-212	5	4
α-helix	214-215	2
α-helix	219-231	13
α-helix	232-236	5
α-helix	237-257	21
α-helix	1003-1011	9
β-strand	1014-1015	2	5
β-strand	1016	1	6
β-strand	1017-1019	3	5
β-strand	1025-1028	4	5
β-strand	1031-1034	4	5
α-helix	1040-1050	11
β-strand	1057	1	6
α-helix	1060-1080	21
α-helix	1085-1090	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	1159-1161	3
α-helix	271-299	29
α-helix	309-333	25
α-helix	335-345	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kappa-type opioid receptor, Lysozyme	A, B	protein	480	Homo Sapiens, Enterobacteria phage T4	P00720, P41145 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4DJH_1 Kappa-type opioid receptor, Lysozyme (chains A, B)
GGTTMGSEDAQLEPAHISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIY
IFNLALADALVTTTMPFQSTVYLMNSWPFGDVLCKIVLSIDYYNMFTSIFTLTMMSVDRY
IAVCHPVKALDFRTPLKAKIINICIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDD
DYSWWDLFMKICVFIFAFVIPVLIIIVCYTLMILRLKSVRLLSGNIFEMLRIDEGLRLKI
YKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRG
ILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSR
WYNQTPNRAKRVITTFRTGTWDAYREKDRNLRRITRLVLVVVAVFVVCWTPIHIFILVEA
LGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTS

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	2
CIT	Citric acid	C6 H8 O7	1
JDC	(3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-y…	C28 H39 N3 O3	2

Water and common crystallization additives (PEG) are not listed.

Primary citation

tructure of the human kappa-opioid receptor in complex with JDTic. Wu, H., Wacker, D., Mileni, M. et al. Nature (2012) 485:327-332. DOI 10.1038/nature10939 · 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…

Browse more

4DJH is part of these collections:

GPCRs and cell signaling

About this viewer

MolViewer shows 4DJH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.