MolNFT v1 · #29877 · protein

Structure of EEF2-eta in complex with PJ34

1ZM9 · Elongation factor 2: “Structure of EEF2-eta in complex with PJ34”. X-ray diffraction, 1 ligand (P34), 20 pockets (best druggability 0.81). MolNFT v1 #29877 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZM9
Type: protein
Length: 3,090 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor 2; Exotoxin a
EC: 2.4.2.36
UniProt: P32324
Ligands: P34
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Elongation factor 2	protein	823	36% helix, 26% strand	P32324
B, D, F	Exotoxin a (EC 2.4.2.36)	protein	207	27% helix, 23% strand	—

Ligands and binding sites

P34 · N~2~,N~2~-dimethyl-N~1~-(6-oxo-5,6-dihydrophenanthridin-2-yl)glycinamide · ligand · 3 copies · chains B, D, F

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1141	0.81	0.82	99	empty
2	839	0.80	0.83	86	empty
3	1010	0.80	0.81	87	empty
4	1142	0.77	0.79	131	empty
5	873	0.74	0.78	93	empty

Interfaces

6 interfaces between chains.

E–F · 857 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 842 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 791 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 308 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 293 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (nonstandard).

Compared structures

1ZM9 · Structure of eEF2-ETA in complex with PJ34 · the same entry in another collection · chain F against F, TM-score 1.00
P32324 · AlphaFold monomer V2.0 prediction for elongation factor 2 (P32324) · a predicted model of the same protein · chain C against A, TM-score 0.66

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 1ZM9 · PDBe 1ZM9 · UniProt P32324

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