Research workbench
Cmp-sialic acid bound structure of the human wild type beta- galactoside alpha-2,6-sialyltransferase 1 (ST6GAL1)
Analyse Cmp-sialic acid bound structure of the human wild type beta- galactoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QVT
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactoside alpha-2,6-sialyltransferase 1
- EC
- 2.4.99.1
- UniProt
- P15907
- Ligands
- NCC
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactoside alpha-2,6-sialyltransferase 1 (EC 2.4.99.1) | protein | 268 | 39% helix, 15% strand | P15907 |
| B | Beta-galactoside alpha-2,6-sialyltransferase 1 (EC 2.4.99.1) | protein | 265 | 40% helix, 15% strand | P15907 |
Ligands and binding sites
- NCC · Cytidine-5'-monophosphate-5-N-acetylneuraminic acid · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.76 | 0.79 | 98 | NCC |
| 2 | 60 | 0.44 | 0.82 | 17 | empty |
| 3 | 57 | 0.39 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 744 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6QVT · CMP-Sialic acid bound structure of the human wild type Beta-galactoside… · the same entry in another collection · chain A against A, TM-score 1.00
- P15907 · AlphaFold monomer V2.0 prediction for beta-galactoside alpha-2,6-sialyltransferase 1… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P15907
- Elsewhere: RCSB PDB 6QVT · PDBe 6QVT · UniProt P15907
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.