MolNFT v1 · #63690 · protein
Structure of endo-beta-N-acetylglucosaminidase a
3FHA: “Structure of endo-beta-N-acetylglucosaminidase a”. X-ray diffraction, 3 ligands (CA, MG, PO4), 20 pockets (best druggability 0.77). MolNFT v1 #63690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FHA
- Type
- protein
- Length
- 2,345 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase
- EC
- 3.2.1.96
- UniProt
- Q9ZB22
- Ligands
- CA, MG, PO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase (EC 3.2.1.96) | protein | 598 | 18% helix, 32% strand | Q9ZB22 |
| B | Endo-beta-N-acetylglucosaminidase (EC 3.2.1.96) | protein | 583 | 18% helix, 32% strand | Q9ZB22 |
| C | Endo-beta-N-acetylglucosaminidase (EC 3.2.1.96) | protein | 592 | 18% helix, 32% strand | Q9ZB22 |
| D | Endo-beta-N-acetylglucosaminidase (EC 3.2.1.96) | protein | 572 | 19% helix, 32% strand | Q9ZB22 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.77 | 0.80 | 83 | GOL, CA |
| 2 | 944 | 0.76 | 0.79 | 93 | empty |
| 3 | 1154 | 0.73 | 0.76 | 98 | empty |
| 4 | 297 | 0.70 | 0.84 | 28 | empty |
| 5 | 563 | 0.68 | 0.78 | 61 | GOL, CA |
Interfaces
3 interfaces between chains.
- B–C · 571 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3FHA · Structure of endo-beta-N-acetylglucosaminidase A · 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 Q9ZB22
- Elsewhere: RCSB PDB 3FHA · PDBe 3FHA · UniProt Q9ZB22
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