MolNFT v1 · #162431 · protein

Escherichia COLI agpase in complex with AMP.

6R8U · Glucose-1-phosphate adenylyltransferase: “Escherichia COLI agpase in complex with AMP.”. Electron microscopy, 1 ligand (AMP), 20 pockets (best druggability 0.88). MolNFT v1 #162431 on GenesisL1: 3D structure, binding sites and…

PDB: 6R8U
Type: protein
Length: 1,700 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: AMP
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 1 distinct chain · 20% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, C	Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)	protein	425	20% helix, 26% strand	P0A6V1

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 4 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.88	0.89	135	AMP
2	1113	0.87	0.89	125	AMP
3	710	0.86	0.90	73	empty
4	307	0.79	0.90	42	empty
5	149	0.77	0.94	31	empty

Interfaces

6 interfaces between chains.

D–C · 1650 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 1648 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 1472 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1470 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1170 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6R8U · Escherichia coli AGPase in complex with AMP. · 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 C 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 6R8U · PDBe 6R8U · UniProt P0A6V1

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