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Crystal structure of GDP-bound EF1ALPHA from pyrococcus horikoshii

Analyse Crystal structure of GDP-bound EF1ALPHA from pyrococcus horikoshii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WYA
Type: protein
Length: 396 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor 1-alpha
UniProt: O59153
Ligands: GDP
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongation factor 1-alpha	protein	396	20% helix, 37% strand	O59153

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.57	0.80	25	empty
2	153	0.43	0.75	20	empty
3	75	0.43	0.80	15	empty
4	70	0.38	0.78	19	empty
5	51	0.28	0.75	14	GDP

Compared structures

3WYA · Crystal structure of GDP-bound EF1alpha from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
O59153 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha (O59153) · a predicted model of the same protein · chain A against A, TM-score 0.55

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 O59153
Elsewhere: RCSB PDB 3WYA · PDBe 3WYA · UniProt O59153

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