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Crystal structure of notf prenyltransferase

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

PDB: 6VY9
Type: protein
Length: 3,168 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxybrevianamide E synthase notf
EC: 2.5.1.109
UniProt: E0Y3X1
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, G, H, F, D, E, C	Deoxybrevianamide E synthase notf (EC 2.5.1.109)	protein	396	41% helix, 20% strand	E0Y3X1

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	523	0.80	0.86	58	empty
2	510	0.80	0.87	65	empty
3	1012	0.80	0.81	120	empty
4	1137	0.80	0.81	130	empty
5	501	0.78	0.86	57	empty

Interfaces

12 interfaces between chains.

B–H · 1165 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1154 Å² buried · 18 hydrogen bonds · protein-protein
F–C · 1153 Å² buried · 17 hydrogen bonds · protein-protein
A–G · 1128 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1076 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6VY9 · Crystal structure of NotF prenyltransferase · the same entry in another collection · chain E against E, TM-score 1.00
E0Y3X1 · AlphaFold monomer V2.0 prediction for deoxybrevianamide E synthase notf (E0Y3X1) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 E0Y3X1
Elsewhere: RCSB PDB 6VY9 · PDBe 6VY9 · UniProt E0Y3X1

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