MolNFT v1 · #113468 · protein
An inactive (D125N) variant of the catalytic domain, BCGH76, of bacillus circulans AMAN6 in complex with alpha-1,6-mannopentaose
5AGD · Alpha-1,6-mannanase: “An inactive (D125N) variant of the catalytic domain, BCGH76, of bacillus circulans AMAN6 in complex with…”. X-ray diffraction, 2 ligands (MAN, BMA), 7 pockets (best druggability 0.64). MolNFT v1 #113468 on…
- PDB
- 5AGD
- Type
- protein
- Length
- 677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannanase
- EC
- 3.2.1.101
- UniProt
- Q9Z4P9
- Ligands
- MAN, BMA
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannanase (EC 3.2.1.101) | protein | 333 | 62% helix, 8% strand | Q9Z4P9 |
| B | Alpha-1,6-mannanase (EC 3.2.1.101) | protein | 344 | 60% helix, 8% strand | Q9Z4P9 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.64 | 0.79 | 31 | empty |
| 2 | 353 | 0.62 | 0.78 | 37 | empty |
| 3 | 205 | 0.51 | 0.77 | 27 | empty |
| 4 | 202 | 0.48 | 0.75 | 20 | empty |
| 5 | 170 | 0.44 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 418 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5AGD · An inactive (D125N) variant of the catalytic domain, BcGH76, of Bacillus circulans Aman6… · the same entry in another collection · chain B against B, 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 Q9Z4P9
- Elsewhere: RCSB PDB 5AGD · PDBe 5AGD · UniProt Q9Z4P9
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