MolNFT v1 · #163935 · protein

Escherichia COLI agpase in complex with AMP.

6SI8 · Glucose-1-phosphate adenylyltransferase: “Escherichia COLI agpase in complex with AMP.”. Electron microscopy, 1 ligand (AMP), 16 pockets (best druggability 0.88). MolNFT v1 #163935 on GenesisL1: 3D structure, binding sites and…

PDB: 6SI8
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: 16 · best druggability 0.88

Structure

electron microscopy · 1 distinct chain · 22% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, C	Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)	protein	425	22% helix, 27% 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

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1081	0.88	0.89	128	AMP
2	1138	0.88	0.89	136	AMP
3	708	0.86	0.90	70	empty
4	1017	0.81	0.82	109	empty
5	355	0.78	0.88	48	empty

Interfaces

6 interfaces between chains.

D–C · 1661 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 1640 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 1440 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1357 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1144 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6SI8 · 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 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 6SI8 · PDBe 6SI8 · UniProt P0A6V1

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