Research workbench
The structure of GH101 from streptococcus pneumoniae TIGR4 in complex with pugt
Analyse The structure of GH101 from streptococcus pneumoniae TIGR4 in complex with pugt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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