MolNFT v1 · #163039 · protein
Golgi alpha-mannosidase II complex with manno-epi-cyclophellitol aziridine
6RQZ · Alpha-mannosidase 2: “Golgi alpha-mannosidase II complex with manno-epi-cyclophellitol aziridine”. X-ray diffraction, 2 ligands (KGH, ZN), 11 pockets (best druggability 0.81). MolNFT v1 #163039 on GenesisL1: 3D structure, binding…
- PDB
- 6RQZ
- Type
- protein
- Length
- 1,014 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
- KGH, ZN
- Pockets
- 11 · best druggability 0.81
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 | 1014 | 24% helix, 30% strand | Q24451 |
Ligands and binding sites
- KGH · (1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 8 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.81 | 0.84 | 107 | EDO, SIN |
| 2 | 127 | 0.80 | 0.98 | 27 | empty |
| 3 | 282 | 0.65 | 0.81 | 32 | empty |
| 4 | 158 | 0.47 | 0.77 | 25 | EDO, KGH |
| 5 | 124 | 0.46 | 0.78 | 25 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6RQZ · GOLGI ALPHA-MANNOSIDASE II complex with Manno-epi-cyclophellitol aziridine · 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 6RQZ · PDBe 6RQZ · UniProt Q24451
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