Research workbench
Structure of the starch branching enzyme I (bei) complexed with maltopentaose from oryza sativa L
Analyse Structure of the starch branching enzyme I (bei) complexed with maltopentaose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VU2
- Type
- protein
- Length
- 1,383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,4-alpha-glucan-branching enzyme, CHLOROPLASTIC/AMYLOPLASTIC
- EC
- 2.4.1.18
- UniProt
- Q01401
- Ligands
- GLC, BGC
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-alpha-glucan-branching enzyme, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.18) | protein | 692 | 33% helix, 22% strand | Q01401 |
| B | 1,4-alpha-glucan-branching enzyme, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.18) | protein | 691 | 33% helix, 22% strand | Q01401 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 10 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.74 | 0.81 | 48 | empty |
| 2 | 468 | 0.72 | 0.81 | 41 | empty |
| 3 | 508 | 0.69 | 0.79 | 44 | GOL |
| 4 | 51 | 0.66 | 0.96 | 19 | empty |
| 5 | 304 | 0.63 | 0.80 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1087 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VU2 · Structure of the Starch Branching Enzyme I (BEI) complexed with maltopentaose from Oryza… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01401 · AlphaFold monomer V2.0 prediction for 1,4-alpha-glucan-branching enzyme… · a predicted model of the same protein · chain B against A, 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 Q01401
- Elsewhere: RCSB PDB 3VU2 · PDBe 3VU2 · UniProt Q01401
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