Research workbench
Selenomethionine derivative of the GH99 endo-alpha-mannosidase from bacteroides thetaiotaomicron
Analyse Selenomethionine derivative of the GH99 endo-alpha-mannosidase from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ACY
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-alpha-mannosidase
- EC
- 3.2.1.130
- UniProt
- Q8A109
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-alpha-mannosidase (EC 3.2.1.130) | protein | 341 | 35% helix, 18% strand | Q8A109 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.69 | 0.78 | 66 | GOL |
| 2 | 213 | 0.52 | 0.77 | 24 | GOL |
| 3 | 250 | 0.52 | 0.75 | 33 | GOL |
| 4 | 53 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 925 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4ACY · Selenomethionine derivative of the GH99 endo-alpha-mannosidase from Bacteroides… · the same entry in another collection · chain B against B, 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 Q8A109
- Elsewhere: RCSB PDB 4ACY · PDBe 4ACY · UniProt Q8A109
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