Research workbench

The crystal structure of iseg

Analyse The crystal structure of iseg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YMR
Type: protein
Length: 3,191 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Formate acetyltransferase
UniProt: Q727N1
Ligands: 8X3
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D, A	Formate acetyltransferase	protein	798	52% helix, 10% strand	Q727N1
C	Formate acetyltransferase	protein	797	51% helix, 10% strand	Q727N1

Ligands and binding sites

8X3 · 2-hydroxyethylsulfonic acid · ligand · 4 copies · chains B, D, C, A
GOL · Glycerol · additive · 6 copies · chains B, A, D, 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.80	0.96	38	empty
2	127	0.80	0.97	32	empty
3	1178	0.79	0.81	88	empty
4	1164	0.78	0.80	102	GOL
5	186	0.61	0.83	28	empty

Interfaces

4 interfaces between chains.

B–C · 1069 Å² buried · 18 hydrogen bonds · protein-protein
D–A · 1016 Å² buried · 14 hydrogen bonds · protein-protein
D–C · 917 Å² buried · 9 hydrogen bonds · protein-protein
B–A · 886 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5YMR · The Crystal Structure of IseG · the same entry in another collection · chain B against B, TM-score 1.00
Q727N1 · AlphaFold monomer V2.0 prediction for isethionate sulfite-lyase (Q727N1) · a predicted model of the same protein · chain C 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 Q727N1
Elsewhere: RCSB PDB 5YMR · PDBe 5YMR · UniProt Q727N1

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