MolNFT v1 · #138938 · protein
Alpha-N-acetylgalactosaminidase nagbb from bifidobacterium bifidum - ligand free
5WZP: “Alpha-N-acetylgalactosaminidase nagbb from bifidobacterium bifidum - ligand free”. X-ray diffraction, 2 ligands (ZN, CA), 12 pockets (best druggability 0.89). MolNFT v1 #138938 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5WZP
- Type
- protein
- Length
- 1,205 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
- ZN, CA
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 603 | 23% helix, 32% strand | G5ELM1 |
| B | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 602 | 24% helix, 31% strand | G5ELM1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.89 | 0.91 | 116 | empty |
| 2 | 264 | 0.56 | 0.77 | 33 | empty |
| 3 | 244 | 0.53 | 0.76 | 37 | empty |
| 4 | 106 | 0.43 | 0.78 | 16 | empty |
| 5 | 113 | 0.40 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2046 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5WZP · Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free · 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 5WZP · PDBe 5WZP · UniProt G5ELM1
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