Research workbench
Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ADP-glucose
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
- 1YP4
- 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
- ADP, ADQ, SO4
- Pockets
- 18 · best druggability 0.83
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 | 432 | 26% helix, 30% strand | P23509 |
| B | Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) | protein | 433 | 22% helix, 29% strand | P23509 |
| C | Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) | protein | 434 | 27% helix, 30% strand | P23509 |
| D | Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) | protein | 426 | 26% helix, 28% strand | P23509 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- ADQ · Adenosine-5'-diphosphate-glucose · ligand · chains B
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.83 | 0.86 | 113 | SO4 |
| 2 | 84 | 0.74 | 0.97 | 20 | empty |
| 3 | 951 | 0.74 | 0.78 | 101 | SO4 |
| 4 | 490 | 0.73 | 0.82 | 58 | SO4, ADQ |
| 5 | 76 | 0.73 | 0.97 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1447 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1430 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 940 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 771 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 312 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1YP4 · Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with… · the same entry in another collection · chain C against C, 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 1YP4 · PDBe 1YP4 · UniProt P23509
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