MolNFT v1 · #24173 · protein

Geometry of triterpene conversion to pentacarbocyclic hopene

1UMP · Squalene--hopene cyclase: “Geometry of triterpene conversion to pentacarbocyclic hopene”. X-ray diffraction, 1 ligand (SQA), 20 pockets (best druggability 0.86). MolNFT v1 #24173 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1UMP
Type: protein
Length: 1,857 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Squalene--hopene cyclase
EC: 5.4.99.17
UniProt: P33247
Ligands: SQA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Squalene--hopene cyclase (EC 5.4.99.17)	protein	619	54% helix, 4% strand	P33247

Ligands and binding sites

SQA · 2-azasqualene · ligand · 3 copies · chains A, B, C
C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 5 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	327	0.86	0.96	49	SQA
2	321	0.85	0.95	50	SQA
3	311	0.85	0.95	50	SQA
4	63	0.70	0.96	16	empty
5	58	0.69	0.96	19	empty

Interfaces

3 interfaces between chains.

A–C · 647 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 633 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 619 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1UMP · Geometry of triterpene conversion to pentacarbocyclic hopene · the same entry in another collection · chain A against A, TM-score 1.00
P33247 · AlphaFold monomer V2.0 prediction for squalene--hopene cyclase (P33247) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P33247
Elsewhere: RCSB PDB 1UMP · PDBe 1UMP · UniProt P33247

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