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Carbohydrate-binding of the starch binding domain of rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose
Analyse Carbohydrate-binding of the starch binding domain of rhizopus oryzae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V8M
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucoamylase a
- EC
- 3.2.1.3
- UniProt
- Q2VC81
- Ligands
- GLC, SO4
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucoamylase a (EC 3.2.1.3) | protein | 106 | 0% helix, 53% strand | Q2VC81 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 28 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.54 | 0.74 | 35 | GLC |
| 2 | 237 | 0.49 | 0.74 | 28 | GLC |
| 3 | 80 | 0.36 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1031 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 319 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 307 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 82 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2V8M · Carbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q2VC81
- Elsewhere: RCSB PDB 2V8M · PDBe 2V8M · UniProt Q2VC81
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