Research workbench
Monoclinic form of trypanosoma cruzi trans-sialidase, in complex with 3-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA)AND lactose
Analyse Monoclinic form of trypanosoma cruzi trans-sialidase, 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
- 1MS0
- Type
- protein
- Length
- 1,246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-sialidase
- EC
- 3.2.1.18
- UniProt
- Q26964
- Ligands
- DAN, BGC, GAL
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trans-sialidase (EC 3.2.1.18) | protein | 623 | 8% helix, 47% strand | Q26964 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.68 | 0.82 | 34 | GAL, DAN |
| 2 | 336 | 0.66 | 0.81 | 36 | GAL, DAN |
| 3 | 289 | 0.60 | 0.79 | 32 | empty |
| 4 | 247 | 0.59 | 0.79 | 38 | empty |
| 5 | 295 | 0.58 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 361 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1MS0 · Monoclinic form of Trypanosoma cruzi trans-sialidase, in complex with… · 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 Q26964
- Elsewhere: RCSB PDB 1MS0 · PDBe 1MS0 · UniProt Q26964
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