MolNFT v1 · #138936 · protein
Alpha-N-acetylgalactosaminidase nagbb from bifidobacterium bifidum - galnac complex
5WZN: “Alpha-N-acetylgalactosaminidase nagbb from bifidobacterium bifidum - galnac complex”. X-ray diffraction, 3 ligands (A2G, ZN, CA), 17 pockets (best druggability 0.89). MolNFT v1 #138936 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WZN
- Type
- protein
- Length
- 1,240 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
- A2G, ZN, CA
- Pockets
- 17 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 621 | 24% helix, 33% strand | G5ELM1 |
| B | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 619 | 22% helix, 33% strand | G5ELM1 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 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
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.89 | 0.90 | 105 | empty |
| 2 | 57 | 0.66 | 0.94 | 23 | empty |
| 3 | 300 | 0.62 | 0.80 | 50 | A2G |
| 4 | 242 | 0.59 | 0.80 | 40 | A2G |
| 5 | 104 | 0.45 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2066 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5WZN · Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - GalNAc 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 5WZN · PDBe 5WZN · UniProt G5ELM1
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