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Structure of the family GH92 inverting mannosidase BT3990 from bacteroides thetaiotaomicron vpi-5482
Analyse Structure of the family GH92 inverting mannosidase BT3990 from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WW0
- Type
- protein
- Length
- 5,891 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-1,2-mannosidase
- UniProt
- Q8A0N1
- Ligands
- SWA, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H | Putative alpha-1,2-mannosidase | protein | 736 | 31% helix, 23% strand | Q8A0N1 |
| C | Putative alpha-1,2-mannosidase | protein | 737 | 30% helix, 24% strand | Q8A0N1 |
| D | Putative alpha-1,2-mannosidase | protein | 738 | 30% helix, 24% strand | Q8A0N1 |
Ligands and binding sites
- SWA · 1S-8AB-octahydro-indolizidine-1A,2A,8B-triol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 17 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.84 | 0.85 | 126 | empty |
| 2 | 1113 | 0.82 | 0.83 | 116 | empty |
| 3 | 937 | 0.81 | 0.82 | 78 | empty |
| 4 | 637 | 0.78 | 0.84 | 71 | CA, SWA |
| 5 | 306 | 0.75 | 0.87 | 42 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1475 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1471 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1453 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 934 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 216 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2WW0 · Structure of the Family GH92 Inverting Mannosidase BT3990 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 Q8A0N1
- Elsewhere: RCSB PDB 2WW0 · PDBe 2WW0 · UniProt Q8A0N1
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