Research workbench
Escherichia COLI agpase in complex with fbp. symmetry applied C2
Analyse Escherichia COLI agpase in complex with fbp. symmetry applied C2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SHJ
- Type
- protein
- Length
- 1,664 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
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 22% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 416 | 21% helix, 26% strand | P0A6V1 |
| A, C | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 416 | 23% helix, 26% 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.87 | 0.90 | 82 | empty |
| 2 | 828 | 0.81 | 0.84 | 87 | FBP |
| 3 | 755 | 0.81 | 0.84 | 76 | FBP |
| 4 | 756 | 0.80 | 0.84 | 71 | FBP |
| 5 | 726 | 0.79 | 0.83 | 66 | FBP |
Interfaces
6 interfaces between chains.
- A–B · 1595 Ų buried · 27 hydrogen bonds · protein-protein
- D–C · 1561 Ų buried · 28 hydrogen bonds · protein-protein
- D–A · 1122 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1088 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 934 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6SHJ · Escherichia coli AGPase in complex with FBP. Symmetry applied C2 · 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 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 6SHJ · PDBe 6SHJ · UniProt P0A6V1
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