MolNFT v1 · #184407 · protein
Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno- configured N-alkyl cyclophellitol aziridine
7OP7 · Beta-mannosidase: “Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno- configured N-alkyl cyclophellitol aziridine”. X-ray diffraction, 3 ligands (VEE, CL, BR), 14 pockets (best druggability 0.77). MolNFT v1 #184407 on…
- PDB
- 7OP7
- Type
- protein
- Length
- 1,677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- UniProt
- Q8AAK6
- Ligands
- VEE, CL, BR
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase | protein | 837 | 22% helix, 36% strand | Q8AAK6 |
| B | Beta-mannosidase | protein | 840 | 24% helix, 36% strand | Q8AAK6 |
Ligands and binding sites
- VEE · (1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 18 copies · chains A, B
- BR · Bromide ion · ion · 13 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.77 | 0.83 | 55 | EDO, BR, CL |
| 2 | 668 | 0.76 | 0.82 | 53 | EDO, BR, CL |
| 3 | 877 | 0.75 | 0.79 | 97 | EDO, BR |
| 4 | 457 | 0.69 | 0.80 | 40 | EDO |
| 5 | 511 | 0.68 | 0.79 | 48 | EDO |
Interfaces
1 interface between chains.
- A–B · 946 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7OP7 · Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured N-alkyl… · 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 Q8AAK6
- Elsewhere: RCSB PDB 7OP7 · PDBe 7OP7 · UniProt Q8AAK6
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