Research workbench

Scytalone dehydratase plus inhibitor 2

Analyse Scytalone dehydratase plus inhibitor 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5STD
Type: protein
Length: 492 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Scytalone dehydratase
EC: 4.2.1.94
UniProt: P56221
Ligands: UNN, CA
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Scytalone dehydratase (EC 4.2.1.94)	protein	164	30% helix, 48% strand	P56221

Ligands and binding sites

UNN · (6,7-difluoro-quinazolin-4-yl)-(1-methyl-2,2-diphenyl-ethyl)-amine · ligand · 3 copies · chains A, B, C
CA · Calcium ion · metal · 3 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	339	0.80	0.90	43	UNN
2	360	0.79	0.89	45	UNN
3	344	0.79	0.89	42	UNN
4	207	0.69	0.86	46	empty
5	88	0.35	0.74	20	empty

Interfaces

3 interfaces between chains.

A–C · 1059 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1055 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1041 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5STD · Scytalone dehydratase plus inhibitor 2 · the same entry in another collection · chain A against A, TM-score 1.00
P56221 · AlphaFold monomer V2.0 prediction for scytalone dehydratase (P56221) · a predicted model of the same protein · chain A 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 P56221
Elsewhere: RCSB PDB 5STD · PDBe 5STD · UniProt P56221

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.