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Crystal structure of archaeal ribosomal protein AP1, apelota, and GTP- bound AEF1A complex

Analyse Crystal structure of archaeal ribosomal protein AP1, apelota, and GTP- bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JI2
Type: protein
Length: 1,587 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor 1-alpha; Protein pelota homolog; Archaeal ribosomal stalk protein AP1
EC: 3.1.-.-
UniProt: Q9YAV0, Q9YAZ5
Ligands: GTP, MG, NA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Elongation factor 1-alpha	protein	432	21% helix, 35% strand	Q9YAV0
B, F	Protein pelota homolog (EC 3.1.-.-)	protein	357	35% helix, 31% strand	Q9YAZ5
X	Archaeal ribosomal stalk protein AP1	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, E
MG · Magnesium ion · metal · 2 copies · chains A, E
NA · Sodium ion · metal · 2 copies · chains A, E

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.86	0.87	118	empty
2	537	0.81	0.87	60	empty
3	496	0.79	0.87	82	empty
4	281	0.63	0.81	33	empty
5	215	0.59	0.81	25	empty

Interfaces

7 interfaces between chains.

A–B · 1845 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1716 Å² buried · 19 hydrogen bonds · protein-protein
B–E · 894 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 874 Å² buried · 12 hydrogen bonds · protein-protein
A–X · 546 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6JI2 · Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex · the same entry in another collection · chain X against X, TM-score 1.00
Q9YAV0 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha (Q9YAV0) · a predicted model of the same protein · chain E against A, TM-score 0.99
Q9YAZ5 · AlphaFold monomer V2.0 prediction for protein pelota homolog (Q9YAZ5) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9YAV0
Every structure of UniProt Q9YAZ5
Elsewhere: RCSB PDB 6JI2 · PDBe 6JI2 · UniProt Q9YAV0 · UniProt Q9YAZ5

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