MolNFT v1 · #163057 · protein
Golgi alpha-mannosidase II in complex with 5-(adamantan-1YL-methoxy)- pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide
6RRJ · Alpha-mannosidase 2: “Golgi alpha-mannosidase II in complex with 5-(adamantan-1YL-methoxy)- pentyl…”. X-ray diffraction, 2 ligands (KFE, ZN), 11 pockets (best druggability 0.79). MolNFT v1 #163057 on GenesisL1: 3D structure, binding…
- PDB
- 6RRJ
- Type
- protein
- Length
- 1,005 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
- KFE, ZN
- Pockets
- 11 · best druggability 0.79
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 | 1005 | 24% helix, 30% strand | Q24451 |
Ligands and binding sites
- KFE · (2~{S},3~{R},4~{S},5~{R})-~{N}-[5-(1-adamantylmethoxy) pentyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl) pyrrolidine-2-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.79 | 0.97 | 28 | empty |
| 2 | 813 | 0.79 | 0.82 | 104 | empty |
| 3 | 266 | 0.65 | 0.82 | 29 | empty |
| 4 | 172 | 0.52 | 0.78 | 30 | KFE |
| 5 | 130 | 0.44 | 0.77 | 21 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6RRJ · GOLGI ALPHA-MANNOSIDASE II in complex with 5-(Adamantan-1yl-methoxy)-pentyl… · 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 6RRJ · PDBe 6RRJ · UniProt Q24451
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