5D5A: PDB entry 5D5A

In meso in situ serial X-ray crystallography structure of the Beta2-adrenergic receptor at 100 K. Determined by X-ray diffraction at 2.48 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 2.48 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 1
Atoms: 3,809
Mol. weight: 60.02 kDa
Ligands: BU1, ACM, PLM, CLR
Released: 13 Jan 2016

Explore 5D5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D5A contains 27 α-helices and 6 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: 27 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	31-60	30
α-helix	62-64	3
α-helix	67-81	15
α-helix	82-86	5
α-helix	87-96	10
α-helix	102-135	34
α-helix	147-170	24
α-helix	179-186	8
α-helix	197-204	8
α-helix	205-209	5
α-helix	210-228	19
α-helix	1003-1010	8
β-strand	1014-1015	2	1
β-strand	1016	1	2
β-strand	1017-1019	3	1
β-strand	1025-1028	4	1
β-strand	1031-1034	4	1
α-helix	1039-1050	12
β-strand	1057	1	2
α-helix	1060-1080	21
α-helix	1085-1090	6
α-helix	1093-1112	20
α-helix	1115-1122	8
α-helix	1126-1133	8
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	1159-1161	3
α-helix	267-298	32
α-helix	305-317	13
α-helix	318-320	3
α-helix	322-325	4
α-helix	326-328	3
α-helix	330-339	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor	A	protein	500	Homo sapiens, Enterobacteria phage T4	P00720, P07550 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5D5A_1 Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor (chains A)
DYKDDDAMGQPGNGSAFLLAPNRSHAPDHDVTQQRDEVWVVGMGIVMSLIVLAIVFGNVL
VITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSID
VLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHW
YRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIF
EMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAE
KLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQK
RWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLC
WLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRS
SLKAYGNGYSSNGNTGEQSG

Ligands and cofactors

ID	Name	Formula	Copies
BU1	1,4-butanediol	C4 H10 O2	2
ACM	Acetamide	C2 H5 N O	1
PLM	Palmitic acid	C16 H32 O2	1
CLR	Cholesterol	C27 H46 O	3
CAU	(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol	C18 H22 N2 O2	1

Water and common crystallization additives (SO4, 12P) are not listed.

Primary citation

In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Huang, C.Y., Olieric, V., Ma, P. et al. Acta Crystallogr D Struct Biol (2016) 72:93-112. DOI 10.1107/S2059798315021683 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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