Research workbench
Structure of the catalytic domain of human endo-alpha-mannosidase manea in complex with nickel
Analyse Structure of the catalytic domain of human endo-alpha-mannosidase manea in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZDC
- Type
- protein
- Length
- 350 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein endo-alpha-1,2-mannosidase
- EC
- 3.2.1.130
- UniProt
- Q5SRI9
- Ligands
- NI
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein endo-alpha-1,2-mannosidase (EC 3.2.1.130) | protein | 350 | 32% helix, 16% strand | Q5SRI9 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.54 | 0.78 | 31 | empty |
| 2 | 184 | 0.44 | 0.74 | 33 | empty |
| 3 | 58 | 0.35 | 0.78 | 17 | empty |
| 4 | 51 | 0.27 | 0.74 | 15 | empty |
Compared structures
- 6ZDC · Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SRI9 · AlphaFold monomer V2.0 prediction for glycoprotein endo- alpha-1,2-mannosidase (Q5SRI9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5SRI9
- Elsewhere: RCSB PDB 6ZDC · PDBe 6ZDC · UniProt Q5SRI9
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