MolNFT v1 · #83244 · protein

The complex structure of hssqs wtih ligand, fspp

3WC9 · Squalene synthase: “The complex structure of hssqs wtih ligand, fspp”. X-ray diffraction, 1 ligand (FPS), 17 pockets (best druggability 0.81). MolNFT v1 #83244 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WC9
Type: protein
Length: 2,003 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Squalene synthase
EC: 2.5.1.21
UniProt: P37268
Ligands: FPS
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Squalene synthase (EC 2.5.1.21)	protein	333	70% helix, 0% strand	P37268
B, C, D, E, F	Squalene synthase (EC 2.5.1.21)	protein	334	68% helix, 0% strand	P37268

Ligands and binding sites

FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 7 copies · chains A, B, C, D, E, F

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.81	0.82	78	FPS
2	941	0.80	0.82	91	empty
3	940	0.80	0.81	73	FPS
4	843	0.79	0.82	72	FPS
5	938	0.78	0.80	69	FPS

Interfaces

11 interfaces between chains.

A–C · 1161 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1040 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 1039 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 999 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 991 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3WC9 · The complex structure of HsSQS wtih ligand, FSPP · the same entry in another collection · chain F against F, TM-score 1.00
P37268 · AlphaFold monomer V2.0 prediction for squalene synthase (P37268) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 P37268
Elsewhere: RCSB PDB 3WC9 · PDBe 3WC9 · UniProt P37268

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