6J21: Human NK1 substance P receptor

Crystal structure of the human NK1 substance P receptor. Determined by X-ray diffraction at 3.2 Å resolution. Released 6 Mar 2019.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 1
Atoms: 3,138
Mol. weight: 51.32 kDa
Ligands: OLC, GBQ
Released: 6 Mar 2019

Explore 6J21 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J21 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	29-58	30
α-helix	66-95	30
α-helix	101-134	34
α-helix	144-167	24
β-strand	169-173	5	1
β-strand	178-182	5	1
α-helix	191-201	11
α-helix	202-206	5
α-helix	207-224	18
α-helix	1002-1009	8
α-helix	1019-1021	3
α-helix	1023-1034	12
α-helix	1041-1046	6
α-helix	1049-1062	14
α-helix	1064-1067	4
α-helix	1071-1078	8
α-helix	1082-1089	8
α-helix	1093-1097	5
α-helix	1099-1111	13
α-helix	1115-1117	3
α-helix	242-269	28
α-helix	270-272	3
α-helix	275-278	4
α-helix	283-308	26
α-helix	310-318	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Substance-P receptor,Endolysin	A	protein	441	Homo sapiens, Enterobacteria phage T4	P00720, P25103 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J21_1 Substance-P receptor,Endolysin (chains A)
DNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHK
RMRTVTNYFLVNLAFADASMAAFNTVVNFTYAVHNEWYYGLFYCKFHNFFPIAAVFASIW
SMTAVAFDRYMAIIHPLQPRLSATATKVVICVIWVLALLLAFPAGYYSTTETMPSRVVCM
IEWPEHPNKIYEKVYHICVTVLIYFLPLLVIGYAYTVVGIRLWASNIFEMLRIDEGGGSG
GDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLR
MLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYHEQVSAKRKVVKMMIVVV
CTFAICWLPFHIFFLLPYINPDLYLKKFIQQVYLAIMWLAMSSTMYNPIIYCCLNDRFRL
GFKHAFRCCPFISAGDYEGLE

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	1
GBQ	5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-flu…	C23 H21 F7 N4 O3	1

Primary citation

Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography. Chen, S., Lu, M., Liu, D. et al. Nat Commun (2019) 10:638-638. DOI 10.1038/s41467-019-08568-5 · 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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