5K5X: Human PDGFRA

Crystal structure of human PDGFRA. Determined by X-ray diffraction at 2.17 Å resolution. Released 17 Aug 2016.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,918
Mol. weight: 40.88 kDa
Released: 17 Aug 2016

Explore 5K5X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K5X contains 22 α-helices and 18 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: 22 helices, 18 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	577-579	3
α-helix	584-586	3
β-strand	587	1	3
α-helix	590-592	3
β-strand	593-601	9	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
β-strand	694	1	5
α-helix	774-776	3
α-helix	778-781	4
β-strand	791	1	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
α-helix	838-840	3
α-helix	843-845	3
β-strand	850-852	3	6
β-strand	855-857	3	6
α-helix	859-861	3
α-helix	864-869	6
α-helix	874-889	16
α-helix	893-894	2
α-helix	903-910	8
α-helix	915-918	4
α-helix	923-932	10
α-helix	937-939	3
α-helix	941-942	2
α-helix	943-951	9
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

>5K5X_1 Platelet-derived growth factor receptor alpha (chains A)
GAMDKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFG
KVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACT
KSGPIYIITEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLS
FTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFL
PVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAK
PDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD

Primary citation

Structural and biochemical studies of the PDGFRA kinase domain. Liang, L., Yan, X.E., Yin, Y. et al. Biochem Biophys Res Commun (2016) 477:667-672. DOI 10.1016/j.bbrc.2016.06.117 · PubMed

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…
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
6JOJ 2.6 Å, Crystal structure of PDGFRA T674I in complex with crenolanib by soaking

Browse structure collections

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