1N7D: Extracellular domain of the LDL receptor

Extracellular domain of the LDL receptor. Determined by X-ray diffraction at 3.7 Å resolution. Released 21 Jan 2003.

Method: X-ray diffraction
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,956
Mol. weight: 88.31 kDa
Ligands: CA, KEG
Released: 21 Jan 2003

Explore 1N7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N7D contains 1 α-helix and 38 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: 1 helix, 38 β-strands

Element	Residues	Length	Sheet
β-strand	219-221	3	1
β-strand	227-229	3	1
β-strand	349	1	2
β-strand	354	1	2
β-strand	363	1	3
β-strand	372	1	3
β-strand	380	1	4
β-strand	390-391	2	4
β-strand	398-399	2	4
β-strand	412-414	3	5
β-strand	419-422	4	5
β-strand	430	1	6
β-strand	431-434	4	5
β-strand	447	1	6
β-strand	458-459	2	7
β-strand	466	1	8
β-strand	468-469	2	7
β-strand	477-480	4	9
β-strand	481	1	8
β-strand	487-490	4	9
β-strand	501-502	2	10
β-strand	511-512	2	10
β-strand	521-522	2	11
β-strand	523	1	10
β-strand	533-534	2	11
β-strand	545-547	3	12
α-helix	552-553	2
β-strand	554-558	5	12
β-strand	563-567	5	12
β-strand	575-577	3	12
β-strand	591-593	3	13
β-strand	596-600	5	13
β-strand	607-611	5	13
β-strand	615-619	5	13
β-strand	633	1	4
β-strand	661	1	14
β-strand	674	1	14
β-strand	682-683	2	15
β-strand	690-691	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor	A	protein	699	Homo sapiens	P01130 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1N7D_1 Low-density lipoprotein receptor (chains A)
AVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVNR
CIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGKCISRQFVCDSDRDCLDGSDEA
SCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEWPQRCRGLYVFQGDSSPCSAFE
FHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDEFQCSDGNCIHGSRQCDREYDC
KDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLDN
NGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEE
GFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRI
YWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIHSNIYWTDSVLGTVSVA
DTKGVKRKTLFREQGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQ
WPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWT
DIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHQLTQPRGVNWCERTTLSNGGCQYLC
LPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	8
KEG	12-tungstophosphate	O40 P W12	3

Primary citation

Structure of the LDL receptor extracellular domain at endosomal pH. Rudenko, G., Henry, L., Henderson, K. et al. Science (2002) 298:2353-2358. DOI 10.1126/science.1078124 · 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…
1IJQ 1.5 Å, Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair
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

Browse structure collections

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