MolNFT v1 · #125362 · protein
Crystal structure of E. COLI ADP-glucose pyrophosphorylase (agpase) in complex with a positive allosteric regulator beta-fructose-1,6- diphosphate (fbp) - AGPASE*FBP
5L6S · Glucose-1-phosphate adenylyltransferase: “Crystal structure of E. COLI ADP-glucose pyrophosphorylase (agpase) in complex with a positive allosteric…”. X-ray diffraction, 2 ligands (FBP, SO4), 20 pockets (best druggability 0.89).…
- PDB
- 5L6S
- Type
- protein
- Length
- 6,214 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate adenylyltransferase
- EC
- 2.7.7.27
- UniProt
- P0A6V1
- Ligands
- FBP, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 16 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 30% helix, 29% strand | P0A6V1 |
| B | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 417 | 29% helix, 29% strand | P0A6V1 |
| C | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 418 | 28% helix, 29% strand | P0A6V1 |
| D | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 402 | 29% helix, 30% strand | P0A6V1 |
| E | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 408 | 29% helix, 28% strand | P0A6V1 |
| F | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 402 | 29% helix, 28% strand | P0A6V1 |
| G | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 30% helix, 29% strand | P0A6V1 |
| H | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 408 | 30% helix, 28% strand | P0A6V1 |
| I | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 29% helix, 29% strand | P0A6V1 |
| J | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 407 | 29% helix, 29% strand | P0A6V1 |
| K | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 30% helix, 29% strand | P0A6V1 |
| L | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 415 | 30% helix, 28% strand | P0A6V1 |
| M | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 229 | 24% helix, 24% strand | P0A6V1 |
| N | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 369 | 30% helix, 25% strand | P0A6V1 |
| O | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 364 | 28% helix, 30% strand | P0A6V1 |
| P | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 339 | 30% helix, 25% strand | P0A6V1 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, C, G, I, K, J, L
- SO4 · Sulfate ion · ion · 39 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.89 | 0.92 | 106 | empty |
| 2 | 1191 | 0.88 | 0.89 | 126 | empty |
| 3 | 898 | 0.87 | 0.90 | 107 | SO4 |
| 4 | 732 | 0.87 | 0.91 | 71 | empty |
| 5 | 841 | 0.87 | 0.90 | 80 | empty |
Interfaces
35 interfaces between chains.
- C–D · 1734 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1691 Ų buried · 28 hydrogen bonds · protein-protein
- I–J · 1678 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1669 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 1571 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5L6S · Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a… · the same entry in another collection · chain K against K, TM-score 1.00
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 5L6S · PDBe 5L6S · UniProt P0A6V1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.