MolNFT v1 · #53486 · protein
Structure of the family GH92 inverting mannosidase BT2199 from bacteroides thetaiotaomicron vpi-5482
2WW2 · Alpha-1,2-mannosidase: “Structure of the family GH92 inverting mannosidase BT2199 from bacteroides thetaiotaomicron vpi-5482”. X-ray diffraction, 2 ligands (SWA, NA), 13 pockets (best druggability 0.81). MolNFT v1 #53486 on…
- PDB
- 2WW2
- Type
- protein
- Length
- 2,211 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,2-mannosidase
- UniProt
- Q8A5N9
- Ligands
- SWA, NA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-1,2-mannosidase | protein | 737 | 31% helix, 23% strand | Q8A5N9 |
Ligands and binding sites
- SWA · 1S-8AB-octahydro-indolizidine-1A,2A,8B-triol · ligand · chains B
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 14 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.81 | 0.82 | 102 | empty |
| 2 | 372 | 0.80 | 0.89 | 46 | GOL |
| 3 | 398 | 0.79 | 0.88 | 56 | GOL |
| 4 | 1093 | 0.79 | 0.81 | 95 | GOL, SWA |
| 5 | 661 | 0.78 | 0.83 | 66 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1024 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1021 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 907 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2WW2 · Structure of the Family GH92 Inverting Mannosidase BT2199 from Bacteroides… · 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 Q8A5N9
- Elsewhere: RCSB PDB 2WW2 · PDBe 2WW2 · UniProt Q8A5N9
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