MolNFT v1 · #163273 · protein
Crystal structure of DFG5 from chaetomium thermophilum in complex with mannose
6RY1 · Mannan endo-1,6-alpha-mannosidase: “Crystal structure of DFG5 from chaetomium thermophilum in complex with mannose”. X-ray diffraction, 2 ligands (MAN, CA), 5 pockets (best druggability 0.48). MolNFT v1 #163273 on GenesisL1: 3D…
- PDB
- 6RY1
- 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
- MAN, CA
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 55% 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 | 55% helix, 4% strand | G0S3F2 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- ACT · Acetate ion · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.48 | 0.77 | 21 | CA, MAN |
| 2 | 97 | 0.47 | 0.80 | 24 | empty |
| 3 | 58 | 0.41 | 0.81 | 15 | empty |
| 4 | 67 | 0.36 | 0.77 | 19 | empty |
| 5 | 51 | 0.33 | 0.78 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6RY1 · Crystal structure of Dfg5 from Chaetomium thermophilum in complex with mannose · 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 6RY1 · PDBe 6RY1 · UniProt G0S3F2
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