Research workbench
The structure of GH101 from streptococcus pneumoniae TIGR4 in complex with 1-O-methyl-T-antigen
Analyse The structure of GH101 from streptococcus pneumoniae TIGR4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A56
- Type
- protein
- Length
- 1,106 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-alpha-N-acetylgalactosaminidase
- EC
- 3.2.1.97
- UniProt
- Q2MGH6
- Ligands
- MGC, GAL, CA, MN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-alpha-N-acetylgalactosaminidase (EC 3.2.1.97) | protein | 1106 | 14% helix, 37% strand | Q2MGH6 |
Ligands and binding sites
- MGC · methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside · ligand · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 31 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.81 | 0.95 | 32 | EDO |
| 2 | 66 | 0.73 | 0.98 | 23 | empty |
| 3 | 81 | 0.59 | 0.88 | 18 | empty |
| 4 | 212 | 0.55 | 0.79 | 24 | empty |
| 5 | 225 | 0.54 | 0.78 | 34 | empty |
Compared structures
- 5A56 · The structure of GH101 from Streptococcus pneumoniae TIGR4 in complex with… · 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 5A56 · PDBe 5A56 · UniProt Q2MGH6
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