MolNFT v1 · #18302 · protein

Structure of a C-kit kinase product complex

1PKG · C-kit protein: “Structure of a C-kit kinase product complex”. X-ray diffraction, 2 ligands (ADP, MG), 5 pockets (best druggability 0.70). MolNFT v1 #18302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PKG
Type: protein
Length: 571 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-kit protein
UniProt: P10721
Ligands: ADP, MG
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-kit protein	protein	292	38% helix, 18% strand	P10721
B	C-kit protein	protein	279	38% helix, 16% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	183	0.70	0.88	31	MG, ADP
2	217	0.69	0.86	33	MG, ADP
3	493	0.63	0.76	48	empty
4	202	0.51	0.77	39	empty
5	121	0.43	0.76	26	empty

Interfaces

1 interface between chains.

A–B · 992 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

1PKG · Structure of a c-Kit Kinase Product Complex · the same entry in another collection · chain A against A, TM-score 1.00
P10721 · AlphaFold monomer V2.0 prediction for MAST/STEM cell growth factor receptor kit (P10721) · a predicted model of the same protein · chain A against A, TM-score 0.88

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P10721
Elsewhere: RCSB PDB 1PKG · PDBe 1PKG · UniProt P10721

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