MolNFT v1 · #83250 · protein

The complex structure of hssqs wtih LIGAND,BPH1218

3WCF · Squalene synthase: “The complex structure of hssqs wtih LIGAND,BPH1218”. X-ray diffraction, 1 ligand (BH8), 17 pockets (best druggability 0.83). MolNFT v1 #83250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WCF
Type: protein
Length: 2,004 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: BH8
Pockets: 17 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Squalene synthase (EC 2.5.1.21)	protein	334	71% helix, 0% strand	P37268

Ligands and binding sites

BH8 · hydrogen [(1S)-2-(3-decyl-1H-imidazol-3-ium-1-yl)-1-phosphonoethyl]phosphonate · ligand · 6 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	1055	0.83	0.84	105	BH8
2	723	0.81	0.85	60	BH8
3	1073	0.81	0.82	109	empty
4	686	0.81	0.85	64	BH8
5	604	0.81	0.86	49	BH8

Interfaces

11 interfaces between chains.

A–C · 1022 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 978 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 976 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 959 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 956 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3WCF · The complex structure of HsSQS wtih ligand,BPH1218 · the same entry in another collection · chain E against E, 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 3WCF · PDBe 3WCF · UniProt P37268

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