MolNFT v1 · #148519 · protein
Structure of the family GH92 alpha-mannosidase BT3965 from bacteroides thetaiotaomicron in complex with mannoimidazole (mani)
6F92 · Putative alpha-1,2-mannosidase: “Structure of the family GH92 alpha-mannosidase BT3965 from bacteroides thetaiotaomicron in complex with…”. X-ray diffraction, 5 ligands (MVL, NA, CA), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6F92
- Type
- protein
- Length
- 3,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-1,2-mannosidase
- UniProt
- A0A139JT15
- Ligands
- MVL, NA, CA, CL, NO3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative alpha-1,2-mannosidase | protein | 760 | 29% helix, 24% strand | A0A139JT15 |
| B | Putative alpha-1,2-mannosidase | protein | 749 | 28% helix, 24% strand | A0A139JT15 |
| C | Putative alpha-1,2-mannosidase | protein | 747 | 28% helix, 24% strand | A0A139JT15 |
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 · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 2 copies · chains D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D
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 | 1141 | 0.84 | 0.85 | 86 | empty |
| 2 | 1132 | 0.83 | 0.84 | 85 | empty |
| 3 | 302 | 0.78 | 0.90 | 69 | empty |
| 4 | 355 | 0.76 | 0.87 | 70 | empty |
| 5 | 551 | 0.74 | 0.82 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2017 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1963 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 733 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 710 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6F92 · Structure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron… · the same entry in another collection · chain C against C, 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 6F92 · PDBe 6F92 · UniProt A0A139JT15
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