MolNFT v1 · #126824 · protein
Crystal structure of alpha-1,2-mannosidase from caulobacter K31 strain in complex with 1-deoxymannojirimycin
5MEH · Mannosyl-oligosaccharide 1,2-alpha-mannosidase: “Crystal structure of alpha-1,2-mannosidase from caulobacter K31 strain in complex with 1-deoxymannojirimycin”. X-ray diffraction, 3 ligands (DMJ, CA, NA), 4 pockets (best druggability…
- PDB
- 5MEH
- Type
- protein
- Length
- 438 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
- DMJ, CA, NA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) | protein | 438 | 51% helix, 13% strand | B0SWV2 |
Ligands and binding sites
- DMJ · 1-deoxymannojirimycin · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 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 | 61 | 0.71 | 0.97 | 18 | empty |
| 2 | 276 | 0.61 | 0.80 | 36 | GOL, CA, DMJ |
| 3 | 104 | 0.48 | 0.81 | 23 | CA |
| 4 | 50 | 0.29 | 0.76 | 17 | ACT |
Compared structures
- 5MEH · Crystal structure of alpha-1,2-mannosidase from Caulobacter K31 strain in complex with… · 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 5MEH · PDBe 5MEH · UniProt B0SWV2
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