Research workbench
Crystal structure of E. COLI ADP-glucose pyrophosphorylase (agpase) in complex with a negative allosteric regulator adenosine monophosphate (AMP) - AGPASE*AMP
Analyse Crystal structure of E. COLI ADP-glucose pyrophosphorylase (agpase) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L6V
- Type
- protein
- Length
- 6,646 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
- AMP, GLC, FRU, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 13 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 422 | 27% helix, 29% strand | P0A6V1 |
| B | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 421 | 28% helix, 29% strand | P0A6V1 |
| C, K | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 421 | 28% helix, 29% strand | P0A6V1 |
| D | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 413 | 29% helix, 29% strand | P0A6V1 |
| E, F | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 29% helix, 29% strand | P0A6V1 |
| G | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 29% helix, 29% strand | P0A6V1 |
| H | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 416 | 28% helix, 28% strand | P0A6V1 |
| I | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 400 | 29% helix, 29% strand | P0A6V1 |
| J | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 29% helix, 28% strand | P0A6V1 |
| L | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 28% helix, 29% strand | P0A6V1 |
| M | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 415 | 29% helix, 27% strand | P0A6V1 |
| O | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 415 | 29% helix, 28% strand | P0A6V1 |
| P | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 423 | 28% helix, 28% strand | P0A6V1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 16 copies · chains A, C, B, D, E, G, F, H, I, K, J, L, M, O, N, P
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, E, G, H, I, J, K, N
- FRU · beta-D-fructofuranose · sugar · 8 copies · chains A, E, G, H, I, J, K, N
- PO4 · Phosphate ion · ion · chains D
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 | 1199 | 0.88 | 0.89 | 156 | AMP |
| 2 | 914 | 0.87 | 0.89 | 112 | AMP |
| 3 | 785 | 0.87 | 0.90 | 76 | empty |
| 4 | 724 | 0.86 | 0.90 | 108 | AMP |
| 5 | 662 | 0.86 | 0.91 | 76 | empty |
Interfaces
33 interfaces between chains.
- C–D · 1519 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 1503 Ų buried · 36 hydrogen bonds · protein-protein
- O–P · 1474 Ų buried · 33 hydrogen bonds · protein-protein
- B–K · 1473 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1468 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5L6V · Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a… · the same entry in another collection · chain D against D, 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 5L6V · PDBe 5L6V · UniProt P0A6V1
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