Research workbench
Crystal structure of rice granule bound starch synthase I catalytic domain
Analyse Crystal structure of rice granule bound starch synthase I catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VUE
- Type
- protein
- Length
- 488 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Granule-bound starch synthase 1, CHLOROPLASTIC/AMYLOPLASTIC
- EC
- 2.4.1.242
- UniProt
- Q0DEV5
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Granule-bound starch synthase 1, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.242) | protein | 488 | 37% helix, 20% strand | Q0DEV5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.74 | 0.81 | 52 | SO4 |
| 2 | 82 | 0.44 | 0.81 | 18 | empty |
| 3 | 118 | 0.39 | 0.74 | 20 | empty |
| 4 | 64 | 0.32 | 0.75 | 17 | empty |
| 5 | 66 | 0.29 | 0.74 | 14 | SO4 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3VUE · Crystal Structure of Rice Granule bound Starch Synthase I Catalytic Domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q0DEV5 · AlphaFold monomer V2.0 prediction for granule-bound starch synthase 1… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q0DEV5
- Elsewhere: RCSB PDB 3VUE · PDBe 3VUE · UniProt Q0DEV5
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