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Structure of the phosphomimetic mutant of ef-tu T383E

Analyse Structure of the phosphomimetic mutant of ef-tu T383E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MI8
Type: protein
Length: 769 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor tu 1
UniProt: A8A5E6
Ligands: GDP, MG, CL
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongation factor tu 1	protein	386	24% helix, 38% strand	A8A5E6
B	Elongation factor tu 1	protein	383	25% helix, 38% strand	A8A5E6

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · chains B
ACT · Acetate ion · additive · 4 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	383	0.62	0.77	67	empty
2	216	0.57	0.79	34	empty
3	115	0.44	0.78	29	empty
4	125	0.34	0.72	23	empty
5	84	0.32	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1319 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5MI8 · Structure of the phosphomimetic mutant of EF-Tu T383E · the same entry in another collection · chain B against B, TM-score 1.00
A8A5E6 · AlphaFold monomer V2.0 prediction for elongation factor tu 1 (A8A5E6) · a predicted model of the same protein · chain B against A, TM-score 0.59

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 A8A5E6
Elsewhere: RCSB PDB 5MI8 · PDBe 5MI8 · UniProt A8A5E6

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