MolNFT v1 · #171696 · protein
Structure of the catalytic domain of human endo-alpha-mannosidase manea in complex with hepes
6ZDF · Glycoprotein endo-alpha-1,2-mannosidase: “Structure of the catalytic domain of human endo-alpha-mannosidase manea in complex with hepes”. X-ray diffraction, 14 pockets (best druggability 0.86). MolNFT v1 #171696 on GenesisL1: 3D…
- PDB
- 6ZDF
- Type
- protein
- Length
- 1,071 residues
- Chains
- 3
- 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
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein endo-alpha-1,2-mannosidase (EC 3.2.1.130) | protein | 356 | 31% helix, 17% strand | Q5SRI9 |
| B | Glycoprotein endo-alpha-1,2-mannosidase (EC 3.2.1.130) | protein | 357 | 31% helix, 16% strand | Q5SRI9 |
| C | Glycoprotein endo-alpha-1,2-mannosidase (EC 3.2.1.130) | protein | 358 | 30% helix, 15% strand | Q5SRI9 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.86 | 0.87 | 99 | empty |
| 2 | 169 | 0.71 | 0.89 | 23 | empty |
| 3 | 216 | 0.70 | 0.87 | 21 | empty |
| 4 | 171 | 0.69 | 0.88 | 20 | empty |
| 5 | 320 | 0.61 | 0.78 | 40 | EPE |
Interfaces
3 interfaces between chains.
- A–C · 659 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 532 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6ZDF · 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 B 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 Q5SRI9
- Elsewhere: RCSB PDB 6ZDF · PDBe 6ZDF · UniProt Q5SRI9
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