MolNFT v1 · #123846 · protein
GH6 orpinomyces sp. Y102 enzyme
5JX5 · Glucanase: “GH6 orpinomyces sp. Y102 enzyme”. X-ray diffraction, 2 ligands (NH4, PO4), 6 pockets (best druggability 0.73). MolNFT v1 #123846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JX5
- 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
- NH4, PO4
- Pockets
- 6 · best druggability 0.73
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
- NH4 · Ammonium ion · ion · 13 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, C, D, B
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.73 | 0.77 | 130 | GOL, NH4, ACT |
| 2 | 812 | 0.71 | 0.77 | 91 | GOL, EDO, NH4 |
| 3 | 279 | 0.59 | 0.78 | 40 | EDO |
| 4 | 58 | 0.46 | 0.84 | 17 | EDO |
| 5 | 64 | 0.32 | 0.76 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–D · 757 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 753 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 286 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5JX5 · 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 5JX5 · PDBe 5JX5 · UniProt A0A076U926
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