MolNFT v1 · #105549 · protein
Crystal structure of sialyltransferase from photobacterium damsela with cmp-3F(A)NEU5AC bound
4R84 · Sialyltransferase 0160: “Crystal structure of sialyltransferase from photobacterium damsela with cmp-3F(A)NEU5AC bound”. X-ray diffraction, 2 ligands (CSF, CA), 9 pockets (best druggability 0.67). MolNFT v1 #105549 on GenesisL1: 3D…
- PDB
- 4R84
- Type
- protein
- Length
- 1,896 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
- CSF, CA
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sialyltransferase 0160 (EC 2.4.99.1) | protein | 474 | 38% helix, 26% strand | O66375 |
Ligands and binding sites
- CSF · Cytidine-5'-monophosphate-3-fluoro-N-acetyl-neuraminic acid · ligand · 4 copies · chains A, B, C, D
- 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.67 | 0.75 | 95 | empty |
| 2 | 281 | 0.54 | 0.76 | 37 | CSF |
| 3 | 277 | 0.54 | 0.76 | 39 | CSF |
| 4 | 278 | 0.53 | 0.75 | 41 | CSF |
| 5 | 275 | 0.53 | 0.75 | 38 | CSF |
Interfaces
4 interfaces between chains.
- A–B · 431 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 426 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 370 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 184 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4R84 · Crystal structure of Sialyltransferase from Photobacterium damsela with CMP-3F(a)Neu5Ac… · the same entry in another collection · chain B against B, 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 4R84 · PDBe 4R84 · UniProt O66375
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