MolNFT v1 · #143106 · protein
Crystal structure of human ST6GALNAC2
6APJ · Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2: “Crystal structure of human ST6GALNAC2”. X-ray diffraction, 1 ligand (NAG), 16 pockets (best druggability 0.78). MolNFT v1 #143106 on GenesisL1: 3D structure, binding…
- PDB
- 6APJ
- Type
- protein
- Length
- 1,737 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
- EC
- 2.4.99.-
- UniProt
- Q9UJ37
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 291 | 41% helix, 10% strand | Q9UJ37 |
| B | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 285 | 41% helix, 12% strand | Q9UJ37 |
| C | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 289 | 42% helix, 10% strand | Q9UJ37 |
| D | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 288 | 41% helix, 10% strand | Q9UJ37 |
| E | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 288 | 40% helix, 10% strand | Q9UJ37 |
| F | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 296 | 40% helix, 10% strand | Q9UJ37 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.78 | 0.86 | 44 | empty |
| 2 | 1077 | 0.77 | 0.79 | 101 | empty |
| 3 | 976 | 0.77 | 0.79 | 97 | empty |
| 4 | 991 | 0.76 | 0.78 | 100 | empty |
| 5 | 414 | 0.73 | 0.83 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–F · 679 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 592 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 452 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 115 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified, 12 disulfide, 4 glycan (engineered, disulfide, N-glycosylation).
Compared structures
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 Q9UJ37
- Elsewhere: RCSB PDB 6APJ · PDBe 6APJ · UniProt Q9UJ37
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