MolNFT v1 · #113098 · protein
The structure of GH101 from streptococcus pneumoniae TIGR4 in complex with pugt
5A57 · Endo-alpha-N-acetylgalactosaminidase: “The structure of GH101 from streptococcus pneumoniae TIGR4 in complex with pugt”. X-ray diffraction, 3 ligands (5G0, GAL, CA), 12 pockets (best druggability 0.80). MolNFT v1 #113098 on…
- PDB
- 5A57
- Type
- protein
- Length
- 1,107 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-alpha-N-acetylgalactosaminidase
- UniProt
- Q2MGH6
- Ligands
- 5G0, GAL, CA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-alpha-N-acetylgalactosaminidase | protein | 1107 | 15% helix, 37% strand | Q2MGH6 |
Ligands and binding sites
- 5G0 · (Z)-[(3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-ylidene]amino] N-phenylcarbamate · ligand · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 23 copies · chains A
- CIT · Citric acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.80 | 0.94 | 34 | EDO |
| 2 | 71 | 0.74 | 0.98 | 22 | empty |
| 3 | 94 | 0.60 | 0.88 | 23 | empty |
| 4 | 216 | 0.60 | 0.80 | 24 | empty |
| 5 | 263 | 0.56 | 0.77 | 39 | empty |
Compared structures
- 5A57 · The structure of GH101 from Streptococcus pneumoniae TIGR4 in complex with PUGT · the same entry in another collection · chain A against A, TM-score 1.00
- Q2MGH6 · AlphaFold monomer V2.0 prediction for endo-alpha-N- acetylgalactosaminidase (Q2MGH6) · a predicted model of the same protein · 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 Q2MGH6
- Elsewhere: RCSB PDB 5A57 · PDBe 5A57 · UniProt Q2MGH6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.