5K2D: PDB entry 5K2D

1.9A angstrom A2a adenosine receptor structure with MR phasing using XFEL data. Determined by X-ray diffraction at 1.9 Å resolution. Released 21 Sept 2016.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 1
Atoms: 3,636
Mol. weight: 58.27 kDa
Ligands: OLA, OLC, OLB, CLR
Released: 21 Sept 2016

Explore 5K2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K2D contains 23 α-helices and 2 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: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-33	32
α-helix	35-37	3
α-helix	40-54	15
α-helix	55-59	5
α-helix	60-67	8
β-strand	71-73	3	1
α-helix	74-107	34
α-helix	109-115	7
α-helix	118-136	19
α-helix	138-141	4
α-helix	151-157	7
β-strand	163-165	3	1
α-helix	168-171	4
α-helix	174-175	2
α-helix	176-187	12
α-helix	188-1019	40
α-helix	1023-1042	20
α-helix	1057-1080	24
α-helix	1084-1092	9
α-helix	1094-1097	4
α-helix	1098-1102	5
α-helix	1103-258	44
α-helix	263-266	4
α-helix	267-291	25
α-helix	293-306	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adenosine receptor A2a/Soluble cytochrome b562 chimera	A	protein	447	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P29274 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5K2D_1 Adenosine receptor A2a/Soluble cytochrome b562 chimera (chains A)
MKTIIALSYIFCLVFADYKDDDDGAPPIMGSSVYITVELAIAVLAILGNVLVCWAVWLNS
NLQNVTNYFVVSLAAADIAVGVLAIPFAITISTGFCAACHGCLFIACFVLVLTQSSIFSL
LAIAIDRYIAIRIPLRYNGLVTGTRAKGIIAICWVLSFAIGLTPMLGWNNCGQPKEGKNH
SQGCGEGQVACLFEDVVPMNYMVYFNFFACVLVPLLLMLGVYLRIFLAARRQLADLEDNW
ETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDI
LVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLQKEVHAAKSLAIIV
GLFALCWLPLHIINCFTFFCPDCSHAPLWLMYLAIVLSHTNSVVNPFIYAYRIREFRQTF
RKIIRSHVLRQQEPFKAHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	11
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	8
OLB	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	2
CLR	Cholesterol	C27 H46 O	3
ZMA	4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethy…	C16 H15 N7 O2	1

Water and common crystallization additives (PEG, NA) are not listed.

Primary citation

Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. Batyuk, A., Galli, L., Ishchenko, A. et al. Sci Adv (2016) 2:e1600292-e1600292. DOI 10.1126/sciadv.1600292 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

Browse structure collections

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