4LP4: Human RAGE VC1 fragment in space group P62

Crystal structure of the human RAGE VC1 fragment in space group P62. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Oct 2013.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,501
Mol. weight: 46.35 kDa
Released: 16 Oct 2013

Explore 4LP4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LP4 contains 12 α-helices and 42 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.

Chains A and B: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	24-29	6	1
β-strand	34-36	3	2
β-strand	48-55	8	1
β-strand	62-64	3	1
α-helix	71-74	4
β-strand	77-78	2	2
β-strand	84-86	3	2
α-helix	91-93	3
β-strand	95-102	8	1
β-strand	108-118	11	1
β-strand	119	1	3
α-helix	120-124	5
β-strand	125-127	3	4
β-strand	132-134	3	5
β-strand	139-149	11	4
β-strand	150	1	3
β-strand	154-159	6	6
β-strand	162-164	3	6
β-strand	171-179	9	4
β-strand	186-194	9	4
α-helix	196-197	2
β-strand	206-211	6	6
α-helix	217-219	3
β-strand	220-221	2	6
α-helix	222-224	3
β-strand	225	1	6
β-strand	228-230	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Advanced glycosylation end product-specific receptor	A, B	protein	212	Homo sapiens	Q15109 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4LP4_1 Advanced glycosylation end product-specific receptor (chains A, B)
GAMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVL
PNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPN
KVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARG
GDPRPTFSCSFSPGLPRHRALRTAPIQPRVWE

Primary citation

Structural insights into the oligomerization mode of the human receptor for advanced glycation end-products. Yatime, L., Andersen, G.R. FEBS J (2013) 280:6556-6568. DOI 10.1111/febs.12556 · PubMed

Other PDB entries of the same protein (UniProt Q15109 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5D7F 1.3 Å, X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide
3O3U 1.5 Å, Crystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE)
6XQ1 1.51 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
6XQ3 1.71 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
6XQ5 1.8 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 1
6XQ7 1.8 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5
6XQ8 1.82 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11
3CJJ 1.85 Å, Crystal structure of human rage ligand-binding domain
6XQ6 1.9 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 11
7LML 2.15 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
4P2Y 2.3 Å, Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse…
6XQ9 2.3 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13

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