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Structure of the GH47 processing alpha-1,2-mannosidase from caulobacter strain K31 in complex with noeuromycin
Analyse Structure of the GH47 processing alpha-1,2-mannosidase from caulobacter strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AYR
- Type
- protein
- Length
- 432 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-oligosaccharide 1,2-alpha-mannosidase
- EC
- 3.2.1.113
- UniProt
- B0SWV2
- Ligands
- IFL, CA, NA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) | protein | 432 | 52% helix, 13% strand | B0SWV2 |
Ligands and binding sites
- IFL · (3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)piperidin-2-one · ligand · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.73 | 0.99 | 18 | empty |
| 2 | 247 | 0.62 | 0.81 | 37 | CA, IFL |
| 3 | 93 | 0.47 | 0.81 | 20 | CA |
| 4 | 51 | 0.27 | 0.74 | 15 | empty |
Compared structures
- 4AYR · Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in… · 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 B0SWV2
- Elsewhere: RCSB PDB 4AYR · PDBe 4AYR · UniProt B0SWV2
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