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Structure of EEF2 in complex with moriniafungin

Analyse Structure of EEF2 in complex with moriniafungin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NPF
Type: protein
Length: 1,635 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor 2
UniProt: P32324
Ligands: MOU, GDP
Pockets: 18 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongation factor 2	protein	822	35% helix, 25% strand	P32324
B	Elongation factor 2	protein	813	35% helix, 26% strand	P32324

Ligands and binding sites

MOU · (1S,4R,5R,9S,11S)-2-({[(2S,5R,6R,7R,9S,10R)-2-(7-carboxyheptyl)-6-hydroxy-10-methoxy-9-methyl-3-oxo-1,4,8-trioxaspiro[4 .5]dec-7-yl]oxy}methyl)-9-formyl-13-isopropyl-5-methyltetracyclo[7.4.0.02,11.04.8]tridec-12-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	792	0.71	0.77	62	empty
2	478	0.65	0.77	48	empty
3	391	0.65	0.78	50	MOU
4	296	0.65	0.81	39	MOU
5	461	0.59	0.74	46	empty

Interfaces

1 interface between chains.

A–B · 167 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2NPF · Structure of eEF2 in complex with moriniafungin · the same entry in another collection · chain B against B, TM-score 1.00
P32324 · AlphaFold monomer V2.0 prediction for elongation factor 2 (P32324) · a predicted model of the same protein · chain B against A, TM-score 0.63

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 P32324
Elsewhere: RCSB PDB 2NPF · PDBe 2NPF · UniProt P32324

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