6JOK: PDGFRA

Crystal structure of PDGFRA in complex with sunitinib by soaking. Determined by X-ray diffraction at 3.8 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,731
Mol. weight: 41.06 kDa
Ligands: B49
Released: 25 Mar 2020

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

Secondary structure: helices and β-sheets

6JOK contains 19 α-helices and 16 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: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	560-561	2	1
β-strand	562-565	4	2
β-strand	572-574	3	2
α-helix	575-576	2
α-helix	577-579	3
α-helix	584-586	3
β-strand	587	1	3
β-strand	594-601	8	3
β-strand	605-613	9	3
β-strand	621-629	9	3
α-helix	635-651	17
β-strand	657	1	4
β-strand	660-664	5	3
β-strand	671-675	5	3
β-strand	680-681	2	4
α-helix	682-688	7
α-helix	778-782	5
α-helix	792-811	20
β-strand	814-815	2	1
α-helix	821-823	3
β-strand	824-827	4	4
β-strand	831-834	4	4
β-strand	850-852	3	5
β-strand	855-857	3	5
α-helix	859-861	3
α-helix	864-869	6
α-helix	874-889	16
α-helix	893-894	2
α-helix	903-911	9
α-helix	915-918	4
α-helix	923-932	10
α-helix	937-939	3
α-helix	941-942	2
α-helix	943-952	10
α-helix	956-971	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet-derived growth factor receptor alpha	A	protein	356	Homo sapiens	P16234 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6JOK_1 Platelet-derived growth factor receptor alpha (chains A)
GAMDKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFG
KVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACT
KSGPIYIITEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLS
FTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFL
PVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAK
PDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD

Ligands and cofactors

ID	Name	Formula	Copies
B49	N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene…	C22 H27 F N4 O2	1

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

Primary citation

Crystal structure of PDGFRA in complex with sunitinib by soaking. Liang, L., Yan, X.E. To be published.

Other PDB entries of the same protein (UniProt P16234 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GRN 1.77 Å, Crystal structure of PDGFRA in Complex with WQ-C-159
8PQJ 1.82 Å, PDGFRA wild-type kinase domain
6A32 1.87 Å, Crystal structure of PDGFRA kinase domain mutant T674I
6JOL 1.9 Å, Crystal structure of PDGFRA in complex with imatinib by co-crystallization
8PQK 2.0 Å, APO crystal structure of PDGFRA-T674I kinase domain
9TFB 2.0 Å, PDGFRA-G680R mutant kinase domain in complex with a 6,7-bis(2-methoxyethoxy)quinazoline-b…
5K5X 2.17 Å, Crystal structure of human PDGFRA
9GZH 2.2 Å, PDGFRA-T674I in complex with covalent ponatinib derivative 19
9TF9 2.2 Å, PDGFRA-G680R mutant kinase domain in complex with avapritinib
9TFA 2.2 Å, PDGFRA-G680R mutant kinase domain in complex with a 6,7-dimethoxyquinazoline-based…
9TFC 2.3 Å, PDGFRA-G680R mutant kinase domain in complex with a 7-methoxyquinazolin-6-ol-based…
8PQH 2.5 Å, PDGFRA T674I mutant kinase domain in complex with avapritinib

Browse structure collections

About this viewer

MolViewer shows 6JOK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.