Research workbench
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
- 2WVX
- Type
- protein
- Length
- 2,945 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-1,2-mannosidase
- UniProt
- Q8A0N1
- Ligands
- CA
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Putative alpha-1,2-mannosidase | protein | 736 | 30% helix, 24% strand | Q8A0N1 |
| B | Putative alpha-1,2-mannosidase | protein | 737 | 30% helix, 24% strand | Q8A0N1 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.79 | 0.81 | 115 | CA, GOL |
| 2 | 665 | 0.66 | 0.75 | 62 | empty |
| 3 | 208 | 0.59 | 0.80 | 36 | CA, GOL |
| 4 | 212 | 0.54 | 0.78 | 31 | CA, GOL |
| 5 | 191 | 0.53 | 0.78 | 33 | CA, GOL |
Interfaces
4 interfaces between chains.
- A–C · 467 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 307 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 108 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 2WVX · 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 2WVX · PDBe 2WVX · UniProt Q8A0N1
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