MolNFT v1 · #163061 · protein
Golgi alpha-mannosidase II in complex with pentyl 2,5-dideoxy-2,5- imino-D-talo-hexonamide
6RRN · Alpha-mannosidase 2: “Golgi alpha-mannosidase II in complex with pentyl 2,5-dideoxy-2,5- imino-D-talo-hexonamide”. X-ray diffraction, 2 ligands (KFT, ZN), 12 pockets (best druggability 0.81). MolNFT v1 #163061 on GenesisL1: 3D…
- PDB
- 6RRN
- Type
- protein
- Length
- 989 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
- KFT, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase 2 (EC 3.2.1.114) | protein | 989 | 25% helix, 30% strand | Q24451 |
Ligands and binding sites
- KFT · (2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-~{N}-pentyl-pyrrolidine-2-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.81 | 0.83 | 112 | SIN |
| 2 | 139 | 0.80 | 0.98 | 32 | empty |
| 3 | 254 | 0.65 | 0.82 | 29 | empty |
| 4 | 180 | 0.53 | 0.79 | 26 | KFT, EDO |
| 5 | 101 | 0.47 | 0.80 | 16 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6RRN · GOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide · 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 6RRN · PDBe 6RRN · UniProt Q24451
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