Research workbench
Escherichia COLI agpase in complex with AMP. symmetry C2
Analyse Escherichia COLI agpase in complex with AMP. symmetry C2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SHQ
- Type
- protein
- Length
- 1,696 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 0.85
Structure
electron microscopy · 1 distinct chain · 20% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, C, B | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 424 | 20% helix, 25% strand | P0A6V1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.85 | 0.92 | 73 | empty |
| 2 | 808 | 0.85 | 0.88 | 88 | AMP |
| 3 | 280 | 0.82 | 0.94 | 56 | empty |
| 4 | 388 | 0.78 | 0.88 | 49 | empty |
| 5 | 317 | 0.77 | 0.88 | 47 | empty |
Interfaces
6 interfaces between chains.
- D–C · 1602 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1591 Ų buried · 34 hydrogen bonds · protein-protein
- D–B · 1478 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1452 Ų buried · 27 hydrogen bonds · protein-protein
- C–B · 1209 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6SHQ · Escherichia coli AGPase in complex with AMP. Symmetry C2 · the same entry in another collection · chain B against B, TM-score 1.00
- P0A6V1 · AlphaFold monomer V2.0 prediction for glucose-1-phosphate adenylyltransferase (P0A6V1) · a predicted model of the same protein · chain D 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 P0A6V1
- Elsewhere: RCSB PDB 6SHQ · PDBe 6SHQ · UniProt P0A6V1
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