MolNFT v1 · #58518 · protein
T cruzi trans-sialidase complex with benzoylated nana derivative
3B69: “T cruzi trans-sialidase complex with benzoylated nana derivative”. X-ray diffraction, 2 ligands (BFN, CL), 4 pockets (best druggability 0.63). MolNFT v1 #58518 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3B69
- Type
- protein
- Length
- 626 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-sialidase
- EC
- 3.2.1.18
- UniProt
- Q26966
- Ligands
- BFN, CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trans-sialidase (EC 3.2.1.18) | protein | 626 | 8% helix, 47% strand | Q26966 |
Ligands and binding sites
- BFN · 5-acetamido-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · chains A
- CL · Chloride ion · ion · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.63 | 0.82 | 32 | BFN, EPE |
| 2 | 252 | 0.56 | 0.78 | 31 | empty |
| 3 | 53 | 0.30 | 0.76 | 14 | empty |
| 4 | 66 | 0.26 | 0.71 | 18 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 3B69 · T cruzi Trans-sialidase complex with benzoylated NANA derivative · 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 Q26966
- Elsewhere: RCSB PDB 3B69 · PDBe 3B69 · UniProt Q26966
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