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Crystal structure of vibrionaceae photobacterium sp. jt-ish-224 2,6- sialyltransferase in a ternary complex with donor product cmp and accepter substrate lactose
Analyse Crystal structure of vibrionaceae photobacterium sp. jt-ish-224 2,6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z4T
- Type
- protein
- Length
- 493 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactoside alpha-2,6-sialyltransferase
- UniProt
- A8QYL1
- Ligands
- C5P, GLC, GAL, MG, PO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactoside alpha-2,6-sialyltransferase | protein | 493 | 36% helix, 24% strand | A8QYL1 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.69 | 0.81 | 42 | GAL, C5P, GOL |
| 2 | 249 | 0.53 | 0.76 | 42 | empty |
| 3 | 54 | 0.27 | 0.74 | 17 | GOL |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2Z4T · Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in… · 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 A8QYL1
- Elsewhere: RCSB PDB 2Z4T · PDBe 2Z4T · UniProt A8QYL1
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