Research workbench
Structure of the family GH92 inverting mannosidase BT3990 from bacteroides thetaiotaomicron vpi-5482 in complex with thiomannobioside
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
- 2WW3
- Type
- protein
- Length
- 4,420 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-1,2-mannosidase
- UniProt
- Q8A0N1
- Ligands
- Z5L, MAN, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Putative alpha-1,2-mannosidase | protein | 736 | 30% helix, 24% strand | Q8A0N1 |
| D, F | Putative alpha-1,2-mannosidase | protein | 738 | 31% helix, 23% strand | Q8A0N1 |
Ligands and binding sites
- Z5L · methyl 2-thio-alpha-D-mannopyranoside · ligand · 6 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.81 | 0.82 | 80 | empty |
| 2 | 933 | 0.81 | 0.82 | 80 | empty |
| 3 | 955 | 0.80 | 0.82 | 84 | empty |
| 4 | 786 | 0.77 | 0.81 | 71 | empty |
| 5 | 121 | 0.69 | 0.91 | 24 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1520 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1518 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1514 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 596 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 184 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WW3 · 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 2WW3 · PDBe 2WW3 · UniProt Q8A0N1
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