MolNFT v1 · #143108 · protein
Crystal structure of human ST6GALNAC2 in complex with cmp
6APL · Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2: “Crystal structure of human ST6GALNAC2 in complex with cmp”. X-ray diffraction, 2 ligands (C5P, NAG), 16 pockets (best druggability 0.80). MolNFT v1 #143108 on GenesisL1…
- PDB
- 6APL
- Type
- protein
- Length
- 1,772 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
- C5P, NAG
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 294 | 40% helix, 11% strand | Q9UJ37 |
| B | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 300 | 38% helix, 11% strand | Q9UJ37 |
| C | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 306 | 37% helix, 10% strand | Q9UJ37 |
| D | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 302 | 42% helix, 11% strand | Q9UJ37 |
| E | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 285 | 41% helix, 11% strand | Q9UJ37 |
| F | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) | protein | 285 | 40% helix, 11% strand | Q9UJ37 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.80 | 0.81 | 102 | C5P |
| 2 | 947 | 0.77 | 0.79 | 83 | C5P |
| 3 | 1048 | 0.75 | 0.78 | 91 | C5P |
| 4 | 540 | 0.74 | 0.82 | 59 | C5P |
| 5 | 498 | 0.73 | 0.82 | 62 | C5P |
Interfaces
6 interfaces between chains.
- B–D · 690 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 552 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 528 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 110 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 11 disulfide, 10 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 6APL · PDBe 6APL · UniProt Q9UJ37
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