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Structure of the family GH92 alpha-mannosidase BT3965 from bacteroides thetaiotaomicron
Analyse Structure of the family GH92 alpha-mannosidase BT3965 from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F91
- Type
- protein
- Length
- 5,928 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-1,2-mannosidase
- UniProt
- A0A139JT15
- Ligands
- NA, CA, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alpha-1,2-mannosidase | protein | 740 | 29% helix, 24% strand | A0A139JT15 |
| B | Putative alpha-1,2-mannosidase | protein | 738 | 30% helix, 24% strand | A0A139JT15 |
| C | Putative alpha-1,2-mannosidase | protein | 747 | 29% helix, 24% strand | A0A139JT15 |
| D | Putative alpha-1,2-mannosidase | protein | 742 | 31% helix, 24% strand | A0A139JT15 |
| E | Putative alpha-1,2-mannosidase | protein | 742 | 31% helix, 24% strand | A0A139JT15 |
| F | Putative alpha-1,2-mannosidase | protein | 736 | 30% helix, 24% strand | A0A139JT15 |
| G | Putative alpha-1,2-mannosidase | protein | 742 | 31% helix, 24% strand | A0A139JT15 |
| H | Putative alpha-1,2-mannosidase | protein | 741 | 31% helix, 24% strand | A0A139JT15 |
Ligands and binding sites
- NA · Sodium ion · metal · 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
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.78 | 0.80 | 86 | empty |
| 2 | 1068 | 0.73 | 0.76 | 79 | empty |
| 3 | 282 | 0.73 | 0.86 | 62 | empty |
| 4 | 58 | 0.72 | 0.98 | 21 | empty |
| 5 | 52 | 0.72 | 0.99 | 19 | empty |
Interfaces
10 interfaces between chains.
- B–E · 1912 Ų buried · 29 hydrogen bonds · protein-protein
- F–G · 1912 Ų buried · 28 hydrogen bonds · protein-protein
- E–H · 838 Ų buried · 12 hydrogen bonds · protein-protein
- D–G · 834 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 560 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6F91 · Structure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron · 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 A0A139JT15
- Elsewhere: RCSB PDB 6F91 · PDBe 6F91 · UniProt A0A139JT15
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