MolNFT v1 · #85457 · protein
Structure of the GH99 endo-alpha-mannosidase from bacteroides xylanisolvens in complex with glucose-1,3-isofagomine
4AD2 · Glycosyl hydrolase family 71: “Structure of the GH99 endo-alpha-mannosidase from bacteroides xylanisolvens in complex with…”. X-ray diffraction, 2 ligands (IFM, GLC), 13 pockets (best druggability 0.78). MolNFT v1 #85457 on…
- PDB
- 4AD2
- Type
- protein
- Length
- 1,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 71
- EC
- 3.2.1.130
- UniProt
- D6D1V7
- Ligands
- IFM, GLC
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 71 (EC 3.2.1.130) | protein | 345 | 35% helix, 17% strand | D6D1V7 |
| B | Glycosyl hydrolase family 71 (EC 3.2.1.130) | protein | 346 | 35% helix, 17% strand | D6D1V7 |
| C | Glycosyl hydrolase family 71 (EC 3.2.1.130) | protein | 344 | 33% helix, 17% strand | D6D1V7 |
| D | Glycosyl hydrolase family 71 (EC 3.2.1.130) | protein | 342 | 33% helix, 18% strand | D6D1V7 |
Ligands and binding sites
- IFM · 5-hydroxymethyl-3,4-dihydroxypiperidine · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.78 | 0.82 | 83 | GLC, IFM |
| 2 | 105 | 0.77 | 0.97 | 26 | empty |
| 3 | 437 | 0.69 | 0.81 | 48 | empty |
| 4 | 145 | 0.60 | 0.84 | 28 | empty |
| 5 | 226 | 0.56 | 0.79 | 33 | empty |
Interfaces
4 interfaces between chains.
- B–D · 644 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 304 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 234 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4AD2 · Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex… · 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 D6D1V7
- Elsewhere: RCSB PDB 4AD2 · PDBe 4AD2 · UniProt D6D1V7
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