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Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ATP
Analyse Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YP3
- Type
- protein
- Length
- 1,725 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate adenylyltransferase small subunit
- EC
- 2.7.7.27
- UniProt
- P23509
- Ligands
- ATP, SO4
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) | protein | 433 | 25% helix, 30% strand | P23509 |
| B | Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) | protein | 432 | 26% helix, 28% strand | P23509 |
| C | Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) | protein | 435 | 26% helix, 29% strand | P23509 |
| D | Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) | protein | 425 | 24% helix, 28% strand | P23509 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 13 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.84 | 0.86 | 116 | SO4 |
| 2 | 536 | 0.76 | 0.83 | 67 | SO4 |
| 3 | 100 | 0.75 | 0.96 | 32 | empty |
| 4 | 554 | 0.75 | 0.82 | 65 | SO4 |
| 5 | 340 | 0.73 | 0.85 | 55 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1538 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1020 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 873 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1YP3 · Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- P23509 · AlphaFold monomer V2.0 prediction for glucose-1-phosphate adenylyltransferase small… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P23509
- Elsewhere: RCSB PDB 1YP3 · PDBe 1YP3 · UniProt P23509
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