MolNFT v1 · #156717 · protein
Crystal structure analysis of plant exohydrolase in complex with methyl 2-thio-beta-sophoroside
6MD6 · Beta-D-glucan exohydrolase isoenzyme exoi: “Crystal structure analysis of plant exohydrolase in complex with methyl 2-thio-beta-sophoroside”. X-ray diffraction, 4 ligands (U2A, NAG, BGC), 2 pockets (best druggability 0.51). MolNFT…
- PDB
- 6MD6
- Type
- protein
- Length
- 604 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-glucan exohydrolase isoenzyme exoi
- UniProt
- A0A287SCR5
- Ligands
- U2A, NAG, BGC, SO4
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-D-glucan exohydrolase isoenzyme exoi | protein | 604 | 38% helix, 12% strand | A0A287SCR5 |
Ligands and binding sites
- U2A · methyl 2-thio-beta-D-glucopyranoside · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 10 copies · chains A
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.51 | 0.83 | 20 | BGC, GOL, 1PE |
| 2 | 65 | 0.33 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MD6 · Crystal structure analysis of plant exohydrolase in complex with methyl… · 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 A0A287SCR5
- Elsewhere: RCSB PDB 6MD6 · PDBe 6MD6 · UniProt A0A287SCR5
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