MolNFT v1 · #161513 · protein

Crystal structure of APT1 bound to palmitic acid.

6QGS · Acyl-protein thioesterase 1: “Crystal structure of APT1 bound to palmitic acid.”. X-ray diffraction, 2 ligands (PLM, CL), 9 pockets (best druggability 0.85). MolNFT v1 #161513 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6QGS
Type: protein
Length: 1,330 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-protein thioesterase 1
EC: 3.1.2.-
UniProt: O75608
Ligands: PLM, CL
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Acyl-protein thioesterase 1 (EC 3.1.2.-)	protein	225	34% helix, 21% strand	O75608
D, A, C, E, F	Acyl-protein thioesterase 1 (EC 3.1.2.-)	protein	221	39% helix, 19% strand	O75608

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains D, A
CL · Chloride ion · ion · chains A

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.85	0.85	129	PLM
2	360	0.80	0.89	69	empty
3	791	0.79	0.82	65	empty
4	1000	0.75	0.78	105	PLM
5	134	0.62	0.85	27	empty

Interfaces

11 interfaces between chains.

C–F · 846 Å² buried · 4 hydrogen bonds · protein-protein
B–A · 835 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 539 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 405 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 374 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6QGS · Crystal structure of APT1 bound to palmitic acid. · the same entry in another collection · chain F against F, TM-score 1.00
O75608 · AlphaFold monomer V2.0 prediction for acyl-protein thioesterase 1 (O75608) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O75608
Elsewhere: RCSB PDB 6QGS · PDBe 6QGS · UniProt O75608

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