1IJQ: LDL Receptor YWTD-EGF Domain Pair

Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair. Determined by X-ray diffraction at 1.5 Å resolution. Released 23 May 2001.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,043
Mol. weight: 71.19 kDa
Released: 23 May 2001

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

Secondary structure: helices and β-sheets

1IJQ contains 5 α-helices and 58 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: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	379-383	5	1
β-strand	385	1	2
β-strand	388-392	5	1
β-strand	399-402	4	1
β-strand	408-414	7	2
β-strand	419-424	6	2
β-strand	429-434	6	2
β-strand	445-448	4	2
β-strand	457-461	5	3
β-strand	466-471	6	3
β-strand	476-481	6	3
β-strand	487-492	6	3
β-strand	498-504	7	4
β-strand	509-514	6	4
β-strand	520-525	6	4
β-strand	531-535	5	4
β-strand	542-548	7	5
β-strand	553-558	6	5
β-strand	563-568	6	5
β-strand	575-579	5	5
β-strand	587-593	7	6
β-strand	596-601	6	6
β-strand	606-611	6	6
β-strand	619-622	4	6
β-strand	631-634	4	1
α-helix	636-638	3
α-helix	652-655	4
β-strand	659-662	4	7
β-strand	673-676	4	7
β-strand	682-683	2	8
β-strand	690-691	2	8

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	379-383	5	9
β-strand	385	1	10
β-strand	388-392	5	9
β-strand	398-402	5	9
β-strand	408-414	7	10
β-strand	419-424	6	10
β-strand	429-433	5	10
β-strand	445-448	4	10
β-strand	457-461	5	11
β-strand	466-471	6	11
β-strand	476-481	6	11
β-strand	487-492	6	11
β-strand	498-504	7	12
β-strand	509-514	6	12
α-helix	519	1
β-strand	520-525	6	12
β-strand	532-535	4	12
β-strand	542-548	7	13
β-strand	553-558	6	13
β-strand	563-568	6	13
β-strand	575-579	5	13
β-strand	587-593	7	14
β-strand	596-601	6	14
β-strand	606-611	6	14
β-strand	619-622	4	14
β-strand	631-634	4	9
α-helix	636-638	3
α-helix	652-655	4
β-strand	659-662	4	15
β-strand	673-676	4	15
β-strand	682-683	2	16
β-strand	690-691	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor	A, B	protein	316	Homo sapiens	P01130 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1IJQ_1 LOW-DENSITY LIPOPROTEIN RECEPTOR (chains A, B)
IAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLD
RAHGVSSYDTVISRDIQAPDGLAVDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGS
KPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQWPNGITLDLLSGRLYW
VDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGS
DVNLLAENLLSPEDMVLFHNLTQPRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCA
CPDGMLLARDMRSCLT

Primary citation

Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair. Jeon, H., Meng, W., Takagi, J. et al. Nat Struct Biol (2001) 8:499-504. DOI 10.1038/88556 · PubMed

Other PDB entries of the same protein (UniProt P01130 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FCW 1.26 Å, Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4…
3SO6 1.37 Å, Crystal structure of the LDL receptor tail in complex with autosomal recessive…
1AJJ 1.7 Å, Ldl receptor ligand-binding module 5, calcium-coordinating
5OYL 2.25 Å, Vsv G CR2
2W2N 2.3 Å, WT PCSK9-deltaC bound to EGF-A H306Y mutant of LDLR
2W2Q 2.33 Å, PCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR
2W2M 2.4 Å, Wt PCSK9-deltac bound to wt egf-a of ldlr
3BPS 2.41 Å, PCSK9:EGF-A complex
4NE9 2.6 Å, PCSK9 in complex with LDLR peptide
2W2O 2.62 Å, PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR
2W2P 2.62 Å, PCSK9-deltaC D374A mutant bound to WT EGF-A of LDLR
3GCW 2.7 Å, PCSK9:EGFA(H306Y)

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