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The complex structure of hssqs wtih ligand, wc-9

Analyse The complex structure of hssqs wtih ligand, wc-9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WCD
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: RWY
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 69% 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	69% helix, 0% strand	P37268

Ligands and binding sites

RWY · 2-(4-phenoxyphenoxy)ethyl thiocyanate · ligand · 4 copies · chains A, B, D, E

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

Pockets

18 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	1146	0.83	0.83	105	empty
2	808	0.81	0.84	94	RWY
3	980	0.80	0.82	98	empty
4	815	0.79	0.82	72	RWY
5	757	0.78	0.82	59	RWY

Interfaces

11 interfaces between chains.

A–C · 1021 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 982 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 971 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 962 Å² buried · 7 hydrogen bonds · protein-protein
D–F · 938 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3WCD · The complex structure of HsSQS wtih ligand, WC-9 · 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 3WCD · PDBe 3WCD · UniProt P37268

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