Research workbench
D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoundecaose
Analyse D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of bacillus circulans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WNP
- Type
- protein
- Length
- 1,398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cycloisomaltooligosaccharide glucanotransferase
- EC
- 2.4.1.248
- UniProt
- P94286
- Ligands
- GLC, BGC, CA, NA, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cycloisomaltooligosaccharide glucanotransferase (EC 2.4.1.248) | protein | 699 | 19% helix, 40% strand | P94286 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.78 | 0.80 | 91 | BGC, GLC |
| 2 | 317 | 0.53 | 0.74 | 39 | GLC |
| 3 | 133 | 0.48 | 0.79 | 20 | MES |
| 4 | 138 | 0.46 | 0.77 | 23 | empty |
| 5 | 139 | 0.45 | 0.77 | 18 | MES |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3WNP · D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of Bacillus circulans T-3040… · the same entry in another collection · chain A against A, TM-score 1.00
- P94286 · AlphaFold monomer V2.0 prediction for cycloisomaltooligosaccharide glucanotransferase… · a predicted model of the same protein · chain A 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 P94286
- Elsewhere: RCSB PDB 3WNP · PDBe 3WNP · UniProt P94286
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.