Research workbench
Structure of the family 32 carbohydrate-binding module from streptococcus pneumoniae endod
Analyse Structure of the family 32 carbohydrate-binding module from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XQX
- Type
- protein
- Length
- 293 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase D
- UniProt
- Q93HW0
- Ligands
- CA
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase D | protein | 147 | 5% helix, 50% strand | Q93HW0 |
| B | Endo-beta-N-acetylglucosaminidase D | protein | 146 | 5% helix, 49% strand | Q93HW0 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.48 | 0.75 | 40 | empty |
| 2 | 136 | 0.41 | 0.75 | 29 | empty |
| 3 | 125 | 0.40 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 721 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2XQX · Structure of the family 32 carbohydrate-binding module from Streptococcus pneumoniae EndoD · 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 Q93HW0
- Elsewhere: RCSB PDB 2XQX · PDBe 2XQX · UniProt Q93HW0
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