MolNFT v1 · #148517 · protein
Structure of the family GH92 alpha-mannosidase BT3130 from bacteroides thetaiotaomicron in complex with mannoimidazole (mani)
6F90 · Alpha-1,2-mannosidase, putative: “Structure of the family GH92 alpha-mannosidase BT3130 from bacteroides thetaiotaomicron in complex with…”. X-ray diffraction, 2 ligands (MVL, CA), 16 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 6F90
- Type
- protein
- Length
- 2,114 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,2-mannosidase, putative
- UniProt
- A0A174L250
- Ligands
- MVL, CA
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,2-mannosidase, putative | protein | 714 | 30% helix, 24% strand | A0A174L250 |
| B | Alpha-1,2-mannosidase, putative | protein | 708 | 31% helix, 24% strand | A0A174L250 |
| C | Alpha-1,2-mannosidase, putative | protein | 692 | 31% helix, 25% strand | A0A174L250 |
Ligands and binding sites
- MVL · (5R,6R,7S,8R)-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.64 | 0.75 | 86 | empty |
| 2 | 71 | 0.61 | 0.90 | 27 | empty |
| 3 | 159 | 0.54 | 0.80 | 34 | CA, MVL |
| 4 | 79 | 0.53 | 0.85 | 20 | empty |
| 5 | 180 | 0.53 | 0.79 | 34 | CA, MVL |
Interfaces
2 interfaces between chains.
- B–C · 1503 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 645 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6F90 · Structure of the family GH92 alpha-mannosidase BT3130 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 A0A174L250
- Elsewhere: RCSB PDB 6F90 · PDBe 6F90 · UniProt A0A174L250
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