MolNFT v1 · #115021 · protein

PH domain of ASAP1 in complex with DIC4-PTDINS(4,5)P2

5C79 · Arf-gap: “PH domain of ASAP1 in complex with DIC4-PTDINS(4,5)P2”. X-ray diffraction, 2 ligands (PBU, CL), 1 pocket (best druggability 0.47). MolNFT v1 #115021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C79
Type: protein
Length: 207 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arf-gap
UniProt: Q9QWY8
Ligands: PBU, CL
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arf-gap	protein	104	26% helix, 39% strand	Q9QWY8
B	Arf-gap	protein	103	22% helix, 40% strand	Q9QWY8

Ligands and binding sites

PBU · (2R)-3-{[(R)-hydroxy{[(1r,2r,3s,4r,5r,6s)-2,3,6-trihydroxy-4,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate · ligand · 3 copies · chains A, B
CL · Chloride ion · ion · chains B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.47	0.74	28	PBU

Interfaces

1 interface between chains.

A–B · 186 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5C79 · PH domain of ASAP1 in complex with diC4-PtdIns(4,5)P2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9QWY8 · AlphaFold monomer V2.0 prediction for arf-gap with SH3 domain, ank repeat and pH… · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9QWY8
Elsewhere: RCSB PDB 5C79 · PDBe 5C79 · UniProt Q9QWY8

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