Research workbench
Golgi alpha-mannosidase II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3, 4-dihydro-2H-1,5-benzodioxepin-7-YL)BENZYL]OXY}PENTYL)-2- (hydroxymethyl)-3,4,5-piperidinetriol
Analyse Golgi alpha-mannosidase II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RRW
- 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
- KG5, 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 | 1005 | 24% helix, 30% strand | Q24451 |
Ligands and binding sites
- KG5 · (2~{R},3~{R},4~{R},5~{S})-1-[5-[[4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)phenyl]methoxy]pentyl]-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · chains A
- ZN · Zinc ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.80 | 0.97 | 29 | empty |
| 2 | 860 | 0.80 | 0.82 | 117 | empty |
| 3 | 265 | 0.64 | 0.82 | 32 | empty |
| 4 | 212 | 0.54 | 0.78 | 31 | KG5 |
| 5 | 133 | 0.47 | 0.78 | 22 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6RRW · GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benz… · 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 6RRW · PDBe 6RRW · UniProt Q24451
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