MolNFT v1 · #29870 · protein

Structure of ADP-ribosylated EEF2 in complex with catalytic fragment of eta

1ZM2 · Elongation factor 2: “Structure of ADP-ribosylated EEF2 in complex with catalytic fragment of eta”. X-ray diffraction, 1 ligand (APR), 20 pockets (best druggability 0.81). MolNFT v1 #29870 on GenesisL1: 3D structure, binding sites…

PDB: 1ZM2
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.-
UniProt: P32324
Ligands: APR
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 25% 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.-)	protein	207	27% helix, 21% strand	—

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · chains E, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.81	0.83	104	empty
2	932	0.79	0.81	72	empty
3	1173	0.77	0.79	130	empty
4	465	0.77	0.85	46	empty
5	1166	0.76	0.79	128	empty

Interfaces

6 interfaces between chains.

E–F · 872 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 845 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 674 Å² buried · 1 hydrogen bond · protein-protein
A–F · 322 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 307 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 1 covalent (nonstandard, covalent ligand).

Compared structures

1ZM2 · Structure of ADP-ribosylated eEF2 in complex with catalytic fragment of ETA · 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 1ZM2 · PDBe 1ZM2 · UniProt P32324

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