5GRN: PDGFRA

Crystal structure of PDGFRA in Complex with WQ-C-159. Determined by X-ray diffraction at 1.77 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 1.77 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,716
Mol. weight: 41.28 kDa
Ligands: 748
Released: 16 Aug 2017

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

Secondary structure: helices and β-sheets

5GRN contains 18 α-helices and 12 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: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	587	1	1
α-helix	590-592	3
β-strand	593-601	9	1
β-strand	605-613	9	1
β-strand	621-629	9	1
α-helix	635-651	17
β-strand	657	1	2
α-helix	658-659	2
β-strand	660-664	5	1
β-strand	671-675	5	1
β-strand	681	1	2
α-helix	682-688	7
α-helix	792-811	20
α-helix	821-823	3
β-strand	824-827	4	2
β-strand	831-834	4	2
α-helix	838-840	3
α-helix	843-845	3
β-strand	850-851	2	3
β-strand	856-857	2	3
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	943-953	11

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

>5GRN_1 Platelet-derived growth factor receptor alpha (chains A)
GAMDKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFG
KVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACT
KSGPIYIITEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLS
FTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFL
PVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAK
PDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD

Ligands and cofactors

ID	Name	Formula	Copies
748	N-[2-(dimethylamino)ethyl]-N-[[4-[[4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)am…	C34 H34 N8 O2	1

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

Primary citation

Crystal Structure of PDGFRA in Complex with WQ-C-159. Yan, X.E., Yun, C.H. To be published.

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

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

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