Research workbench
Alpha-N-acetylgalactosaminidase nagbb from bifidobacterium bifidum - gal-nhac-dnj complex
Analyse Alpha-N-acetylgalactosaminidase nagbb from bifidobacterium bifidum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZR
- Type
- protein
- Length
- 1,260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-acetylgalactosaminidase
- EC
- 3.2.1.49
- UniProt
- G5ELM1
- Ligands
- DJN, ZN, CA
- Pockets
- 16 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 630 | 23% helix, 31% strand | G5ELM1 |
| B | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 630 | 23% helix, 28% strand | G5ELM1 |
Ligands and binding sites
- DJN · N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl) piperidin-3-yl]acetamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.89 | 0.91 | 113 | empty |
| 2 | 58 | 0.63 | 0.93 | 22 | empty |
| 3 | 233 | 0.61 | 0.81 | 44 | DJN |
| 4 | 237 | 0.57 | 0.79 | 43 | DJN |
| 5 | 201 | 0.55 | 0.79 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2078 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5WZR · Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex · 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 G5ELM1
- Elsewhere: RCSB PDB 5WZR · PDBe 5WZR · UniProt G5ELM1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.