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The structure of E. COLI purf in complex with ppgpp-mg

Analyse The structure of E. COLI purf in complex with ppgpp-mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CZF
Type: protein
Length: 1,985 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amidophosphoribosyltransferase
EC: 2.4.2.14
UniProt: P0AG16
Ligands: G4P, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Amidophosphoribosyltransferase (EC 2.4.2.14)	protein	498	35% helix, 23% strand	P0AG16
B	Amidophosphoribosyltransferase (EC 2.4.2.14)	protein	495	34% helix, 23% strand	P0AG16
D	Amidophosphoribosyltransferase (EC 2.4.2.14)	protein	494	34% helix, 23% strand	P0AG16

Ligands and binding sites

G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains A, C, B, D
MG · Magnesium ion · metal · 2 copies · chains A, C, B, D

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	998	0.85	0.86	102	empty
2	1080	0.85	0.86	95	empty
3	1100	0.82	0.83	95	G4P
4	1146	0.82	0.83	88	G4P
5	146	0.71	0.90	44	empty

Interfaces

6 interfaces between chains.

A–B · 2785 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2740 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 1477 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 1338 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 350 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6CZF · The structure of E. coli PurF in complex with ppGpp-Mg · the same entry in another collection · chain A against A, TM-score 1.00
P0AG16 · AlphaFold monomer V2.0 prediction for amidophosphoribosyltransferase (P0AG16) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 P0AG16
Elsewhere: RCSB PDB 6CZF · PDBe 6CZF · UniProt P0AG16

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