MolNFT v1 · #27094 · protein
Crystal structure of human class I alpha-1,2-mannosidase in complex with thio-disaccharide substrate analogue
1X9D · Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha…: “Crystal structure of human class I alpha-1,2-mannosidase in complex with thio-disaccharide substrate analogue”. X-ray diffraction, 4 ligands (Z5L, MAN, CA), 2 pockets (best…
- PDB
- 1X9D
- Type
- protein
- Length
- 451 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha- mannosidase
- EC
- 3.2.1.113
- UniProt
- Q9UKM7
- Ligands
- Z5L, MAN, CA, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha- mannosidase (EC 3.2.1.113) | protein | 451 | 50% helix, 13% strand | Q9UKM7 |
Ligands and binding sites
- Z5L · methyl 2-thio-alpha-D-mannopyranoside · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- BU1 · 1,4-butanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.63 | 0.84 | 22 | Z5L, MAN, CA |
| 2 | 55 | 0.44 | 0.84 | 16 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1X9D · Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKM7 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum mannosyl- oligosaccharide… · a predicted model of the same protein · 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 Q9UKM7
- Elsewhere: RCSB PDB 1X9D · PDBe 1X9D · UniProt Q9UKM7
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