MolNFT v1 · #144211 · protein

Palmitoyltransferase structure

6BMS: “Palmitoyltransferase structure”. X-ray diffraction, 4 ligands (PLM, POV, ZN), 7 pockets (best druggability 0.82). MolNFT v1 #144211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6BMS
Type: protein
Length: 563 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Palmitoyltransferase
EC: 2.3.1.225
UniProt: F1QXD3
Ligands: PLM, POV, ZN, PO4
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Palmitoyltransferase (EC 2.3.1.225)	protein	281	53% helix, 8% strand	F1QXD3
D	Palmitoyltransferase (EC 2.3.1.225)	protein	282	55% helix, 8% strand	F1QXD3

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains A, D
POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains A
ZN · Zinc ion · metal · 4 copies · chains A, D
PO4 · Phosphate ion · ion · 3 copies · chains A, D
LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains A, D

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	632	0.82	0.86	58	PLM
2	392	0.78	0.86	41	PLM
3	80	0.41	0.79	18	PO4
4	80	0.39	0.77	14	empty
5	66	0.36	0.77	13	empty

Interfaces

1 interface between chains.

A–D · 701 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6BMS · Palmitoyltransferase structure · the same entry in another collection · chain A against A, TM-score 1.00
F1QXD3 · AlphaFold monomer V2.0 prediction for palmitoyltransferase ZDHHC15B (F1QXD3) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 F1QXD3
Elsewhere: RCSB PDB 6BMS · PDBe 6BMS · UniProt F1QXD3

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