4XNW: The human P2Y1 receptor

The human P2Y1 receptor in complex with MRS2500. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 Apr 2015.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Clostridium pasteurianum
Chains: 2
Atoms: 5,639
Mol. weight: 96.19 kDa
Ligands: 2ID, ZN
Released: 1 Apr 2015

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

Secondary structure: helices and β-sheets

4XNW contains 53 α-helices and 18 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: 27 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	48	1
α-helix	49-53	5
α-helix	54-79	26
α-helix	81	1
α-helix	83-84	2
α-helix	85-101	17
α-helix	104-112	9
α-helix	120-154	35
α-helix	160-163	4
α-helix	165-183	19
α-helix	185-189	5
β-strand	191-194	4	1
α-helix	199	1
β-strand	200-203	4	1
α-helix	208-210	3
α-helix	211-222	12
α-helix	223-227	5
α-helix	228-246	19
α-helix	1001-1003	3
β-strand	1004-1006	3	2
α-helix	1011	1
β-strand	1012-1013	2	2
β-strand	1019	1	3
α-helix	1020-1022	3
β-strand	1024	1	3
α-helix	1030-1032	3
β-strand	1038	1	4
β-strand	1045	1	4
α-helix	1046-1048	3
β-strand	1049-1051	3	2
α-helix	253-268	16
α-helix	269-273	5
α-helix	274-289	16
α-helix	296-312	17
α-helix	313-315	3
α-helix	316-326	11

Chain C: 26 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	49-79	31
α-helix	83-84	2
α-helix	85-101	17
α-helix	104-112	9
α-helix	120-154	35
α-helix	160-163	4
α-helix	165-183	19
α-helix	185-189	5
β-strand	191-194	4	5
α-helix	199	1
β-strand	200-203	4	5
α-helix	208-210	3
α-helix	211-222	12
α-helix	223-227	5
α-helix	228-246	19
α-helix	1001-1003	3
β-strand	1004-1006	3	6
α-helix	1011	1
β-strand	1012-1013	2	6
β-strand	1019	1	7
α-helix	1020-1022	3
β-strand	1024	1	7
α-helix	1030-1032	3
β-strand	1038	1	8
β-strand	1045	1	8
α-helix	1046-1048	3
β-strand	1049-1051	3	6
α-helix	253-268	16
α-helix	269-273	5
α-helix	274-289	16
α-helix	296-312	17
α-helix	313-315	3
α-helix	316-326	11
α-helix	329-330	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1	A, C	protein	421	Homo sapiens, Clostridium pasteurianum	P00268 (AlphaFold model), P47900 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4XNW_1 P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1 (chains A, C)
TEVLWPAVPNGTDAAFLAGPGSSWGNSTVASTAAVSSSFKCALTKTGFQFYYLPAVYILV
FIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGD
AMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVV
AISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIV
RALIYKMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE
PLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGL
ASLNSCVNPILYFLAGDTFRRRLSRATRKASRRSEANLQSKSEDMTLNILPEFKQNGDTS
L

Ligands and cofactors

ID	Name	Formula	Copies
2ID	[(1R,2S,4S,5S)-4-[2-iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo…	C13 H18 I N5 O8 P2	2
ZN	Zinc ion	Zn	2

Primary citation

Two disparate ligand-binding sites in the human P2Y1 receptor. Zhang, D., Gao, Z.G., Zhang, K. et al. Nature (2015) 520:317-321. DOI 10.1038/nature14287 · PubMed

Other PDB entries of the same protein (UniProt P00268 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PVE 0.79 Å, NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of…
1IRO 1.1 Å, Rubredoxin (oxidized, fe(iii)) at 1.1 Å resolution
1IRN 1.2 Å, Rubredoxin (ZN-substituted) at 1.2 Å resolution
4RXN 1.2 Å, Crystallographic refinement of rubredoxin at 1.2 Å resolution
5RXN 1.2 Å, Combined crystallographic refinement and energy minimization of rubredoxin at 1.2 Å…
1SMM 1.36 Å, Crystal Structure of Cp Rd L41A mutant in oxidized state
1SMW 1.38 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 2 (soaked)
1SMU 1.43 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 1 (drop-reduced)
1B13 1.5 Å, Clostridium pasteurianum rubredoxin G10A mutant
1FHH 1.5 Å, X-ray crystal structure of oxidized rubredoxin
1FHM 1.5 Å, X-ray crystal structure of reduced rubredoxin
1R0I 1.5 Å, cadmium-substituted rubredoxin

Browse structure collections

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