Research workbench
Crystal structure of sialyltransferase from photobacterium damsela
Analyse Crystal structure of sialyltransferase from photobacterium damsela in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R83
- Type
- protein
- Length
- 1,895 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialyltransferase 0160
- EC
- 2.4.99.1
- UniProt
- O66375
- Ligands
- CA
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Sialyltransferase 0160 (EC 2.4.99.1) | protein | 474 | 38% helix, 26% strand | O66375 |
| B | Sialyltransferase 0160 (EC 2.4.99.1) | protein | 473 | 38% helix, 25% strand | O66375 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.60 | 0.74 | 75 | empty |
| 2 | 331 | 0.57 | 0.76 | 45 | empty |
| 3 | 310 | 0.57 | 0.76 | 41 | empty |
| 4 | 220 | 0.55 | 0.78 | 34 | empty |
| 5 | 255 | 0.52 | 0.75 | 33 | empty |
Interfaces
4 interfaces between chains.
- C–D · 403 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 385 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 209 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4R83 · Crystal structure of Sialyltransferase from Photobacterium damsela · 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 O66375
- Elsewhere: RCSB PDB 4R83 · PDBe 4R83 · UniProt O66375
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