5T1A: PDB entry 5T1A

Structure of CC Chemokine Receptor 2 with Orthosteric and Allosteric Antagonists. Determined by X-ray diffraction at 2.81 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 2.81 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 1
Atoms: 3,580
Mol. weight: 59.58 kDa
Ligands: 73R, ZN, OLC, VT5
Released: 14 Dec 2016

Explore 5T1A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T1A contains 26 α-helices and 8 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: 26 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	38-69	32
α-helix	76-92	17
α-helix	95-103	9
α-helix	110-142	33
α-helix	146-151	6
α-helix	154-170	17
α-helix	173-177	5
β-strand	179-184	6	1
β-strand	187-192	6	1
α-helix	196-207	12
α-helix	208-212	5
α-helix	213-228	16
α-helix	1003-1010	8
β-strand	1014-1015	2	2
β-strand	1016	1	3
β-strand	1017-1019	3	2
α-helix	1020	1
β-strand	1025-1028	4	2
β-strand	1031-1034	4	2
α-helix	1039-1050	12
β-strand	1057	1	3
α-helix	1060-1078	19
α-helix	1085-1089	5
α-helix	1093-1111	19
α-helix	1115-1122	8
α-helix	1126-1133	8
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	1162-235	3
α-helix	237-265	29
α-helix	269-272	4
α-helix	279-295	17
α-helix	301-308	8
α-helix	310-319	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimera protein of CC chemokine receptor type 2 isoform B and T4-lysozyme,Lysozyme	A	protein	508	Homo sapiens, Enterobacteria phage T4	P00720, P41597 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5T1A_1 Chimera protein of CC chemokine receptor type 2 isoform B and T4-lysozyme,Lysozyme (chains A)
DYKDDDDKPGTLSTSRSRFIRNTNESGEEVTTFFDYDYGAPCHKFDVKQIGAQLLPPLYS
LVFIFGFVGNMLVVLILINCKKLKCLTDIYLLNLAISDLLFLITLPLWAHSAANEWVFGN
AMCKLFTGLYHIGYFGGIFFIILLTIDRYLAIVHAVFALKARTVTFGVVTSVITWLVAVF
ASVPGIIFTKCQKEDSVYVCGPYFPRGWNNFHTIMRNILGLVLPLLIMVICYSGISRASK
SRINIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVI
TKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL
RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYPPPSREKKAVRVIFTIM
IVYFLFWTPYNIVILLNTFQEFFGLSNCESTSQLDQATQVTETLGMTHCCINPIIYAFVG
EKFRRYLSVFFRKHITKRFGRPLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
73R	(3S)-1-{(1S,2R,4R)-4-[methyl(propan-2-yl)amino]-2-propylcyclohexyl}-3-{[6-(trif…	C26 H36 F3 N5 O	1
ZN	Zinc ion	Zn	1
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	1
VT5	(2~{R})-1-(4-chloranyl-2-fluoranyl-phenyl)-2-cyclohexyl-3-ethanoyl-4-oxidanyl-2…	C18 H19 Cl F N O3	1

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

Primary citation

Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Zheng, Y., Qin, L., Zacarias, N.V. et al. Nature (2016) 540:458-461. DOI 10.1038/nature20605 · 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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