4RWD: PDB entry 4RWD

XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide. Determined by X-ray diffraction at 2.7 Å resolution. Released 14 Jan 2015.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 4
Atoms: 6,326
Mol. weight: 95.69 kDa
Ligands: OLA, OLC
Released: 14 Jan 2015

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

Secondary structure: helices and β-sheets

4RWD contains 42 α-helices and 4 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: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1002-1018	17
α-helix	1023-1041	19
α-helix	1046-1048	3
α-helix	1056-1080	25
α-helix	1084-1101	18
α-helix	1103-1105	3
α-helix	41-42	2
α-helix	43-76	34
α-helix	78-80	3
α-helix	83-100	18
α-helix	102-111	10
α-helix	117-151	35
α-helix	153-159	7
α-helix	162-186	25
β-strand	187-192	6	1
β-strand	195-200	6	1
α-helix	202-203	2
α-helix	206-218	13
α-helix	219-223	5
α-helix	224-241	18
α-helix	250-286	37
α-helix	294-321	28
α-helix	323-332	10

Chain B: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1003-1018	16
α-helix	1023-1041	19
α-helix	1046-1048	3
α-helix	1056-1080	25
α-helix	1084-1101	18
α-helix	1103-1105	3
α-helix	41-42	2
α-helix	43-76	34
α-helix	78-80	3
α-helix	83-100	18
α-helix	102-111	10
α-helix	117-151	35
α-helix	153-159	7
α-helix	162-186	25
β-strand	187-192	6	2
β-strand	195-200	6	2
α-helix	202	1
α-helix	206-218	13
α-helix	219-223	5
α-helix	224-241	18
α-helix	250-286	37
α-helix	294-321	28
α-helix	323-331	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Delta-type opioid receptor	A, B	protein	411	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P41143 (AlphaFold model)
bifunctional peptide	G, H	protein	5	synthetic construct

Sequence of entity 1 (A, B), FASTA

>4RWD_1 Soluble cytochrome b562,Delta-type opioid receptor (chains A, B)
GGTTMADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDS
PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGARSASSLA
LAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSA
KYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKL
INICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPIL
IITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLV
DIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLCRKPCG

Sequence of entity 2 (G, H), FASTA

>4RWD_2 bifunctional peptide (chains G, H)
YXFFX

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	7
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	3

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

Primary citation

Structural basis for bifunctional peptide recognition at human delta-opioid receptor. Fenalti, G., Zatsepin, N.A., Betti, C. et al. Nat Struct Mol Biol (2015) 22:265-268. DOI 10.1038/nsmb.2965 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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