MolNFT v1 · #119857 · protein
Crystal structure analysis of the starch-binding domain of glucoamylase from aspergillus niger
5GHL: “Crystal structure analysis of the starch-binding domain of glucoamylase from aspergillus niger”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.58). MolNFT v1 #119857 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GHL
- Type
- protein
- Length
- 432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucoamylase
- EC
- 3.2.1.3
- UniProt
- P69328
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucoamylase (EC 3.2.1.3) | protein | 108 | 6% helix, 48% strand | P69328 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.58 | 0.75 | 29 | SO4 |
| 2 | 265 | 0.55 | 0.77 | 29 | empty |
| 3 | 172 | 0.45 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 348 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GHL · Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus… · the same entry in another collection · chain D against D, TM-score 1.00
- P69328 · AlphaFold monomer V2.0 prediction for glucoamylase (P69328) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P69328
- Elsewhere: RCSB PDB 5GHL · PDBe 5GHL · UniProt P69328
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