Research workbench
Golgi alpha-mannosidase II complex with (2R,3R,4S)-2-({[(1S)-2- hydroxy-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-diol
Analyse Golgi alpha-mannosidase II complex with (2R,3R,4S)-2-({[(1S)-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F1A
- Type
- protein
- Length
- 1,015 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-mannosidase II
- EC
- 3.2.1.114
- Ligands
- GB2, NAG, ZN, PO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase II (EC 3.2.1.114) | protein | 1015 | 24% helix, 30% strand | — |
Ligands and binding sites
- GB2 · (2R,3R,4S)-2-({[(1S)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.80 | 0.98 | 29 | empty |
| 2 | 815 | 0.79 | 0.82 | 117 | PO4 |
| 3 | 262 | 0.62 | 0.80 | 33 | empty |
| 4 | 238 | 0.53 | 0.76 | 33 | GB2 |
| 5 | 122 | 0.48 | 0.79 | 15 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2F1A · GOLGI ALPHA-MANNOSIDASE II COMPLEX WITH (2R,3R,4S)-2-({[(1S)-2-hydroxy-1-phenylethyl]amino… · 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
- Elsewhere: RCSB PDB 2F1A · PDBe 2F1A
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