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Structure of the bifunctional rel enzyme from B. subtilis

Analyse Structure of the bifunctional rel enzyme from B. subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YXA
Type: protein
Length: 536 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP pyrophosphokinase
EC: 2.7.6.5
UniProt: O54408
Ligands: MN
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP pyrophosphokinase (EC 2.7.6.5)	protein	536	55% helix, 10% strand	O54408

Ligands and binding sites

MN · Manganese (II) ion · metal · chains A

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	454	0.76	0.85	45	empty
2	308	0.71	0.84	29	empty
3	503	0.62	0.75	53	empty
4	149	0.52	0.79	24	empty
5	194	0.48	0.75	28	empty

Compared structures

6YXA · Structure of the bifunctional Rel enzyme from B. subtilis · the same entry in another collection · chain A against A, TM-score 1.00
O54408 · AlphaFold monomer V2.0 prediction for GTP pyrophosphokinase (O54408) · a predicted model of the same protein · chain A 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 O54408
Elsewhere: RCSB PDB 6YXA · PDBe 6YXA · UniProt O54408

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