MolNFT v1 · #113096 · protein
The native structure of GH101 from streptococcus pneumoniae TIGR4
5A55 · Endo-alpha-N-acetylgalactosaminidase: “The native structure of GH101 from streptococcus pneumoniae TIGR4”. X-ray diffraction, 2 ligands (CA, MN), 11 pockets (best druggability 0.80). MolNFT v1 #113096 on GenesisL1: 3D structure…
- PDB
- 5A55
- Type
- protein
- Length
- 1,100 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
- CA, MN
- Pockets
- 11 · best druggability 0.80
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 | 1100 | 14% helix, 37% strand | Q2MGH6 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · 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 | 183 | 0.80 | 0.95 | 31 | empty |
| 2 | 58 | 0.72 | 0.99 | 20 | empty |
| 3 | 241 | 0.58 | 0.79 | 25 | empty |
| 4 | 140 | 0.53 | 0.81 | 26 | empty |
| 5 | 211 | 0.52 | 0.77 | 30 | EDO |
Compared structures
- 5A55 · The native structure of GH101 from Streptococcus pneumoniae TIGR4 · 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 5A55 · PDBe 5A55 · UniProt Q2MGH6
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