Research workbench
Crystal structure of ecoli branching enzyme with gamma cyclodextrin
Analyse Crystal structure of ecoli branching enzyme with gamma cyclodextrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E70
- Type
- protein
- Length
- 2,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,4-alpha-glucan branching enzyme glgb
- EC
- 2.4.1.18
- UniProt
- A7ZSW5
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 586 | 28% helix, 25% strand | A7ZSW5 |
| B | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 600 | 29% helix, 25% strand | A7ZSW5 |
| C | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 578 | 28% helix, 25% strand | A7ZSW5 |
| D | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 588 | 29% helix, 26% strand | A7ZSW5 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 40 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.86 | 0.89 | 73 | empty |
| 2 | 298 | 0.77 | 0.89 | 39 | empty |
| 3 | 306 | 0.77 | 0.89 | 35 | empty |
| 4 | 234 | 0.76 | 0.90 | 53 | GOL |
| 5 | 350 | 0.73 | 0.85 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 954 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 917 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 548 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 118 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5E70 · Crystal structure of Ecoli Branching Enzyme with gamma cyclodextrin · the same entry in another collection · chain D against D, TM-score 1.00
- A7ZSW5 · AlphaFold monomer V2.0 prediction for 1,4-alpha-glucan branching enzyme glgb (A7ZSW5) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 A7ZSW5
- Elsewhere: RCSB PDB 5E70 · PDBe 5E70 · UniProt A7ZSW5
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