1DKF: Protein

Crystal structure of a heterodimeric complex of rar and rxr ligand-binding domains. Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Apr 2000.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 3,743
Mol. weight: 53.3 kDa
Ligands: OLA, BMS
Released: 19 Apr 2000

Explore 1DKF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DKF contains 30 α-helices and 7 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: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	231-234	4
α-helix	237-246	10
α-helix	269-282	14
α-helix	284-289	6
α-helix	299-321	23
β-strand	328-330	3	1
β-strand	336-338	3	1
α-helix	339-344	6
α-helix	348-354	7
α-helix	355-359	5
α-helix	360-364	5
α-helix	369-380	12
α-helix	391-412	22
α-helix	419-424	6
α-helix	426-438	13
α-helix	447-449	3
α-helix	452-461	10

Chain B: 15 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	183-198	16
α-helix	202-204	3
α-helix	205-207	3
β-strand	208	1	2
α-helix	222-245	24
α-helix	254-274	21
β-strand	277-278	2	3
β-strand	283-285	3	3
β-strand	290	1	2
β-strand	291-293	3	3
α-helix	294-297	4
α-helix	298-302	5
α-helix	303-305	3
α-helix	306-315	10
α-helix	317-319	3
α-helix	323-334	12
α-helix	345-366	22
α-helix	373-378	6
α-helix	380-401	22
α-helix	410-415	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (retinoid X receptor-alpha)	A	protein	233	Mus musculus	P28700 (AlphaFold model)
Protein (retinoic acid receptor-alpha)	B	protein	235	Homo sapiens	P10276 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1DKF_1 PROTEIN (RETINOID X RECEPTOR-ALPHA) (chains A)
SANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAK
RIPHFSELPLDDQVILLRAGWNELLIASASHRSIAVKDGILLATGLHVHRNSAHSAGVGA
IFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYC
KHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA

Sequence of entity 2 (B), FASTA

>1DKF_2 PROTEIN (RETINOIC ACID RECEPTOR-ALPHA) (chains B)
PEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVE
FAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAG
FGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKV
YVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	1
BMS	4-[(4,4-dimethyl-1,2,3,4-tetrahydro-[1,2']BINAPTHALENYL-7-carbonyl)-amino]-benz…	C29 H26 N2 O3	1

Primary citation

Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. Bourguet, W., Vivat, V., Wurtz, J.M. et al. Mol Cell (2000) 5:289-298. DOI 10.1016/S1097-2765(00)80424-4 · PubMed

Other PDB entries of the same protein (UniProt P28700 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7PDQ 1.58 Å, Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with…
7AOS 2.55 Å, crystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex…
8J54 2.72 Å, Crystal structure of RXR/DR2 complex
3A9E 2.75 Å, Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha…
7QAA 2.76 Å, Crystal structure of RARalpha/RXRalpha ligand binding domain heterodimer in complex with…
1XDK 2.9 Å, Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex…
7PDT 3.3 Å, Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with…

Browse structure collections

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