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E.COLI phosphoribosylpyrophosphate (prpp) synthetase type a filament bound with ADP, pi and R5P

Analyse E.COLI phosphoribosylpyrophosphate (prpp) synthetase type a filament bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7XMU
Type: protein
Length: 1,842 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribose-phosphate pyrophosphokinase
EC: 2.7.6.1
UniProt: P0A717
Ligands: ADP, HSX, MG, PO4
Pockets: 16 · best druggability 0.78

Structure

electron microscopy · 1 distinct chain · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, B, E, F, C	Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)	protein	307	35% helix, 25% strand	P0A717

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, F, C, D, B, E
HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 6 copies · chains A, D, B, E, F, C
MG · Magnesium ion · metal · 12 copies · chains A, D, B, E, F, C
PO4 · Phosphate ion · ion · 6 copies · chains A, D, C, B, E, F

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

Pockets

16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	908	0.78	0.80	98	HSX, MG, ADP
2	1192	0.76	0.79	107	HSX, MG, ADP
3	1191	0.75	0.78	112	HSX, MG, ADP
4	110	0.34	0.73	20	empty
5	57	0.34	0.77	16	empty

Interfaces

12 interfaces between chains.

B–E · 1993 Å² buried · 22 hydrogen bonds · protein-protein
A–F · 1990 Å² buried · 22 hydrogen bonds · protein-protein
D–C · 1982 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1798 Å² buried · 24 hydrogen bonds · protein-protein
D–B · 1789 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

7XMU · E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A filament bound with ADP, Pi… · the same entry in another collection · chain B against B, TM-score 1.00
P0A717 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase (P0A717) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0A717
Elsewhere: RCSB PDB 7XMU · PDBe 7XMU · UniProt P0A717

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