Research workbench
The structure of axcesd octamer complexed with cellopentaose
Analyse The structure of axcesd octamer complexed with cellopentaose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A8E
- Type
- protein
- Length
- 613 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulose synthase operon protein D
- UniProt
- P37719
- Ligands
- BGC
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cellulose synthase operon protein D | protein | 148 | 43% helix, 16% strand | P37719 |
| B | Cellulose synthase operon protein D | protein | 158 | 39% helix, 16% strand | P37719 |
| C | Cellulose synthase operon protein D | protein | 159 | 40% helix, 17% strand | P37719 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.69 | 0.74 | 80 | BGC |
| 2 | 99 | 0.44 | 0.79 | 16 | empty |
| 3 | 87 | 0.43 | 0.79 | 16 | empty |
| 4 | 67 | 0.34 | 0.76 | 13 | empty |
| 5 | 57 | 0.30 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1525 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1501 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 431 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3A8E · The structure of AxCesD octamer complexed with cellopentaose · the same entry in another collection · chain D against D, TM-score 1.00
- P37719 · AlphaFold monomer V2.0 prediction for cellulose synthase operon protein D (P37719) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P37719
- Elsewhere: RCSB PDB 3A8E · PDBe 3A8E · UniProt P37719
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