Research workbench
Crystal structure of GAN4C, a GH4 6-phospho-glucosidase from geobacillus stearothermophilus
Analyse Crystal structure of GAN4C, a GH4 6-phospho-glucosidase from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C3M
- Type
- protein
- Length
- 1,640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 6-phospho-beta-glucosidase
- EC
- 3.2.1.86
- UniProt
- W8R9V4
- Ligands
- MN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 410 | 50% helix, 17% strand | W8R9V4 |
| B | Putative 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 411 | 51% helix, 17% strand | W8R9V4 |
| C | Putative 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 410 | 50% helix, 18% strand | W8R9V4 |
| D | Putative 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 409 | 51% helix, 16% strand | W8R9V4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.76 | 0.79 | 91 | empty |
| 2 | 736 | 0.75 | 0.80 | 87 | empty |
| 3 | 908 | 0.75 | 0.78 | 92 | empty |
| 4 | 799 | 0.75 | 0.79 | 83 | empty |
| 5 | 55 | 0.72 | 0.99 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1649 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1641 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 70 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C3M · Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus… · 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 W8R9V4
- Elsewhere: RCSB PDB 5C3M · PDBe 5C3M · UniProt W8R9V4
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