6XQ1: PDB entry 6XQ1

Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-((4-(4-carboxyphenoxy)benzyl)oxy)phenyl)-1H-indole-2-carboxylic acid. Determined by X-ray diffraction at 1.51 Å resolution. Released 14 Jul 2021.

Method: X-ray diffraction
Resolution: 1.51 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,900
Mol. weight: 47.73 kDa
Ligands: V74
Released: 14 Jul 2021

Explore 6XQ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XQ1 contains 14 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.

Chain A: 7 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
α-helix	165	1
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

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	24-29	6	7
β-strand	34-36	3	8
β-strand	49-55	7	7
β-strand	62-64	3	7
α-helix	71-74	4
β-strand	77-78	2	8
β-strand	84-86	3	8
α-helix	91-93	3
β-strand	95-102	8	7
β-strand	108-118	11	7
β-strand	119	1	9
α-helix	120-124	5
β-strand	125-127	3	10
β-strand	132-134	3	11
β-strand	139-149	11	10
β-strand	150	1	9
β-strand	154-159	6	12
β-strand	162-163	2	12
α-helix	164-165	2
β-strand	171-179	9	10
β-strand	186-194	9	10
α-helix	196-197	2
β-strand	206-211	6	12
α-helix	217-219	3
β-strand	220-221	2	12
α-helix	222-224	3
β-strand	225	1	12
β-strand	228-230	3	11

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

>6XQ1_1 Advanced glycosylation end product-specific receptor (chains A, B)
GAMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVL
PNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPN
KVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARG
GDPRPTFSCSFSPGLPRHRALRTAPIQPRVWE

Ligands and cofactors

ID	Name	Formula	Copies
V74	3-[3-({[3-(4-carboxyphenoxy)phenyl]methoxy}methyl)phenyl]-1H-indole-2-carboxyli…	C30 H23 N O6	2

Water and common crystallization additives (CL, ACT) are not listed.

Primary citation

A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors. Kozlyuk, N., Gilston, B.A., Salay, L.E. et al. Proteins (2021) 89:1399-1412. DOI 10.1002/prot.26162 · 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)
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
9S2X 2.35 Å, Crystal structure of the human RAGE ectodomain in complex with murine S100A6 mutant Y84C

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