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Bacillus subtilis ffh in complex with ppgpp

Analyse Bacillus subtilis ffh in complex with ppgpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7O9F
Type: protein
Length: 896 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Signal recognition particle protein
UniProt: P37105
Ligands: G4P, MG
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Signal recognition particle protein	protein	300	54% helix, 13% strand	P37105
B	Signal recognition particle protein	protein	301	54% helix, 13% strand	P37105
C	Signal recognition particle protein	protein	295	50% helix, 12% strand	P37105

Ligands and binding sites

G4P · Guanosine-5',3'-tetraphosphate · ligand · 3 copies · chains A, C, B
MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

14 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	911	0.76	0.79	83	G4P
2	199	0.71	0.88	32	empty
3	226	0.49	0.74	32	empty
4	143	0.48	0.78	15	empty
5	125	0.47	0.79	25	G4P, MG

Interfaces

3 interfaces between chains.

B–C · 431 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 425 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 418 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7O9F · Bacillus subtilis Ffh in complex with ppGpp · the same entry in another collection · chain A against A, TM-score 1.00
P37105 · AlphaFold monomer V2.0 prediction for signal recognition particle protein (P37105) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P37105
Elsewhere: RCSB PDB 7O9F · PDBe 7O9F · UniProt P37105

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