MolNFT v1 · #161511 · protein

Crystal structure of APT1 C2S mutant bound to palmitic acid.

6QGQ · Acyl-protein thioesterase 1: “Crystal structure of APT1 C2S mutant bound to palmitic acid.”. X-ray diffraction, 1 ligand (PLM), 5 pockets (best druggability 0.81). MolNFT v1 #161511 on GenesisL1: 3D structure, binding sites and…

PDB: 6QGQ
Type: protein
Length: 888 residues
Chains: 4
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
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acyl-protein thioesterase 1 (EC 3.1.2.-)	protein	223	37% helix, 20% strand	O75608
B	Acyl-protein thioesterase 1 (EC 3.1.2.-)	protein	223	36% helix, 22% strand	O75608
C, D	Acyl-protein thioesterase 1 (EC 3.1.2.-)	protein	221	36% helix, 21% strand	O75608

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains B, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	416	0.81	0.89	71	PLM
2	1096	0.80	0.82	100	empty
3	280	0.80	0.92	60	PLM
4	91	0.37	0.75	18	empty
5	51	0.25	0.72	14	empty

Interfaces

5 interfaces between chains.

A–B · 855 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 831 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 385 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 335 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 298 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6QGQ · Crystal structure of APT1 C2S mutant bound to palmitic acid. · the same entry in another collection · chain A against A, TM-score 1.00
O75608 · AlphaFold monomer V2.0 prediction for acyl-protein thioesterase 1 (O75608) · a predicted model of the same protein · chain C 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 6QGQ · PDBe 6QGQ · UniProt O75608

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