Research workbench

Escherichia COLI agpase in complex with fbp.

Analyse Escherichia COLI agpase in complex with fbp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R8B
Type: protein
Length: 1,688 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose-1-phosphate adenylyltransferase
EC: 2.7.7.27
UniProt: P0A6V1
Ligands: FBP
Pockets: 17 · best druggability 0.87

Structure

electron microscopy · 1 distinct chain · 24% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B, A, C	Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)	protein	422	24% helix, 27% strand	P0A6V1

Ligands and binding sites

FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains D, B, A, C

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

Pockets

17 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	670	0.87	0.91	69	empty
2	1154	0.85	0.86	120	FBP
3	1121	0.85	0.86	119	FBP
4	743	0.78	0.82	68	empty
5	308	0.76	0.88	46	empty

Interfaces

6 interfaces between chains.

D–C · 1664 Å² buried · 28 hydrogen bonds · protein-protein
B–A · 1661 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1054 Å² buried · 11 hydrogen bonds · protein-protein
D–A · 1050 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 982 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6R8B · Escherichia coli AGPase in complex with FBP. · the same entry in another collection · chain C against C, TM-score 1.00
P0A6V1 · AlphaFold monomer V2.0 prediction for glucose-1-phosphate adenylyltransferase (P0A6V1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P0A6V1
Elsewhere: RCSB PDB 6R8B · PDBe 6R8B · UniProt P0A6V1

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