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D308A mutant of bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with cycloisomaltooctaose
Analyse D308A mutant of bacillus circulans T-3040 cycloisomaltooligosaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WNO
- Type
- protein
- Length
- 1,399 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, CA, NA, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cycloisomaltooligosaccharide glucanotransferase (EC 2.4.1.248) | protein | 700 | 20% helix, 41% strand | P94286 |
| B | Cycloisomaltooligosaccharide glucanotransferase (EC 2.4.1.248) | protein | 699 | 20% helix, 40% strand | P94286 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 36 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 · 13 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.74 | 0.77 | 90 | GLC |
| 2 | 305 | 0.54 | 0.74 | 37 | EDO |
| 3 | 260 | 0.50 | 0.74 | 37 | EDO |
| 4 | 253 | 0.48 | 0.73 | 26 | EDO |
| 5 | 120 | 0.46 | 0.79 | 19 | MES |
Interfaces
1 interface between chains.
- A–B · 531 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3WNO · D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase… · 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 3WNO · PDBe 3WNO · UniProt P94286
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