MolNFT v1 · #163915 · protein
Escherichia COLI agpase in complex with fbp. symmetry C1
6SHN · Glucose-1-phosphate adenylyltransferase: “Escherichia COLI agpase in complex with fbp. symmetry C1”. Electron microscopy, 1 ligand (FBP), 18 pockets (best druggability 0.90). MolNFT v1 #163915 on GenesisL1: 3D structure, binding…
- PDB
- 6SHN
- Type
- protein
- Length
- 1,644 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
- 18 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, C, B | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 27% helix, 27% strand | P0A6V1 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains D, B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.90 | 0.92 | 134 | empty |
| 2 | 1076 | 0.85 | 0.86 | 108 | FBP |
| 3 | 383 | 0.76 | 0.86 | 50 | empty |
| 4 | 417 | 0.73 | 0.83 | 61 | empty |
| 5 | 442 | 0.69 | 0.81 | 37 | empty |
Interfaces
6 interfaces between chains.
- D–C · 1672 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1477 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 1133 Ų buried · 16 hydrogen bonds · protein-protein
- D–A · 1118 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 974 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6SHN · Escherichia coli AGPase in complex with FBP. Symmetry C1 · 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 6SHN · PDBe 6SHN · UniProt P0A6V1
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