MolNFT v1 · #152316 · protein
GH6 orpinomyces sp. Y102 enzyme
6IDW · Glucanase: “GH6 orpinomyces sp. Y102 enzyme”. X-ray diffraction, 2 ligands (BGC, PO4), 8 pockets (best druggability 0.76). MolNFT v1 #152316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IDW
- Type
- protein
- Length
- 1,288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucanase
- EC
- 3.2.1.-
- UniProt
- A0A076U926
- Ligands
- BGC, PO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucanase (EC 3.2.1.-) | protein | 322 | 39% helix, 13% strand | A0A076U926 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.76 | 0.80 | 114 | BGC, GOL |
| 2 | 822 | 0.72 | 0.77 | 93 | BGC |
| 3 | 387 | 0.69 | 0.82 | 59 | BGC, GOL |
| 4 | 445 | 0.63 | 0.77 | 48 | BGC, GOL |
| 5 | 69 | 0.47 | 0.83 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 772 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 766 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 270 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 259 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6IDW · GH6 Orpinomyces sp. Y102 enzyme · 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 A0A076U926
- Elsewhere: RCSB PDB 6IDW · PDBe 6IDW · UniProt A0A076U926
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