Research workbench
Crystal structure of DFG5 from chaetomium thermophilum in complex with glucosamine
Analyse Crystal structure of DFG5 from chaetomium thermophilum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RY6
- Type
- protein
- Length
- 410 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan endo-1,6-alpha-mannosidase
- EC
- 3.2.1.101
- UniProt
- G0S3F2
- Ligands
- PA1, CA
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannan endo-1,6-alpha-mannosidase (EC 3.2.1.101) | protein | 410 | 54% helix, 4% strand | G0S3F2 |
Ligands and binding sites
- PA1 · 2-amino-2-deoxy-alpha-D-glucopyranose · ligand · chains A
- CA · Calcium ion · metal · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.52 | 0.81 | 33 | empty |
| 2 | 155 | 0.48 | 0.77 | 24 | PA1 |
| 3 | 58 | 0.41 | 0.81 | 15 | empty |
| 4 | 73 | 0.37 | 0.78 | 19 | empty |
| 5 | 55 | 0.34 | 0.78 | 18 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6RY6 · Crystal structure of Dfg5 from Chaetomium thermophilum in complex with glucosamine · 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 G0S3F2
- Elsewhere: RCSB PDB 6RY6 · PDBe 6RY6 · UniProt G0S3F2
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