MolNFT v1 · #163073 · protein
Golgi alpha-mannosidase II in complex with (2S,3S,4R,5R)-1-(2- (BENZYLOXY)ETHYL)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-triol
6RS0 · Alpha-mannosidase 2: “Golgi alpha-mannosidase II in complex with (2S,3S,4R,5R)-1-(2…”. X-ray diffraction, 2 ligands (KGB, ZN), 10 pockets (best druggability 0.80). MolNFT v1 #163073 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6RS0
- Type
- protein
- Length
- 998 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-mannosidase 2
- EC
- 3.2.1.114
- UniProt
- Q24451
- Ligands
- KGB, ZN
- Pockets
- 10 · 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 2 (EC 3.2.1.114) | protein | 998 | 24% helix, 30% strand | Q24451 |
Ligands and binding sites
- KGB · (2~{S},3~{S},4~{R})-2-(hydroxymethyl)-1-(2-phenylmethoxyethyl)piperidine-3,4,5-triol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.80 | 0.83 | 107 | empty |
| 2 | 129 | 0.79 | 0.97 | 28 | empty |
| 3 | 266 | 0.64 | 0.82 | 33 | empty |
| 4 | 161 | 0.50 | 0.78 | 22 | KGB |
| 5 | 121 | 0.45 | 0.78 | 18 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6RS0 · GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3S,4R,5R)-1-(2-(Benzyloxy)ethyl)-2-(hydroxy… · 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 Q24451
- Elsewhere: RCSB PDB 6RS0 · PDBe 6RS0 · UniProt Q24451
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