MolNFT v1 · #117398 · protein
Crystal structure of E.COLI branching enzyme in complex with alpha cyclodextrin
5E6Y · 1,4-alpha-glucan branching enzyme glgb: “Crystal structure of E.COLI branching enzyme in complex with alpha cyclodextrin”. X-ray diffraction, 1 ligand (GLC), 20 pockets (best druggability 0.79). MolNFT v1 #117398 on GenesisL1: 3D…
- PDB
- 5E6Y
- Type
- protein
- Length
- 2,354 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 0.79
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 587 | 26% helix, 21% strand | A7ZSW5 |
| B | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 594 | 28% helix, 25% strand | A7ZSW5 |
| C | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 584 | 29% helix, 26% strand | A7ZSW5 |
| D | 1,4-alpha-glucan branching enzyme glgb (EC 2.4.1.18) | protein | 589 | 29% helix, 25% strand | A7ZSW5 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 54 copies · chains A, D, B, C
- GOL · Glycerol · additive · 5 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.79 | 0.89 | 39 | empty |
| 2 | 336 | 0.78 | 0.89 | 40 | empty |
| 3 | 327 | 0.78 | 0.89 | 40 | empty |
| 4 | 301 | 0.77 | 0.89 | 37 | empty |
| 5 | 182 | 0.74 | 0.91 | 36 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1042 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 996 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 528 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5E6Y · Crystal structure of E.Coli branching enzyme in complex with alpha 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 5E6Y · PDBe 5E6Y · UniProt A7ZSW5
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