MolNFT v1 · #163072 · protein
Golgi alpha-mannosidase II in complex with (2S,3R)-2-(hydroxymethyl)- 1,2,3,6-tetrahydro-3-pyridinol
6RRY · Alpha-mannosidase 2: “Golgi alpha-mannosidase II in complex with (2S,3R)-2-(hydroxymethyl)- 1,2,3,6-tetrahydro-3-pyridinol”. X-ray diffraction, 2 ligands (KGE, ZN), 9 pockets (best druggability 0.80). MolNFT v1 #163072 on GenesisL1…
- PDB
- 6RRY
- Type
- protein
- Length
- 1,000 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
- KGE, ZN
- Pockets
- 9 · best druggability 0.80
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 | 1000 | 25% helix, 30% strand | Q24451 |
Ligands and binding sites
- KGE · (2~{S},3~{R})-2-(hydroxymethyl)-1,2,3,6-tetrahydropyridin-3-ol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.80 | 0.83 | 112 | SIN, EDO |
| 2 | 127 | 0.79 | 0.97 | 29 | empty |
| 3 | 268 | 0.65 | 0.82 | 30 | empty |
| 4 | 122 | 0.49 | 0.80 | 23 | empty |
| 5 | 154 | 0.47 | 0.77 | 20 | KGE |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6RRY · GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-1,2,3,6-tetrahydro-3… · 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 6RRY · PDBe 6RRY · UniProt Q24451
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