Research workbench
Crystal structure of the drosophila melanogaster polypeptide N- acetylgalactosaminyl transferase PGANT9B
Analyse Crystal structure of the drosophila melanogaster polypeptide N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E4R
- Type
- protein
- Length
- 999 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase 9
- EC
- 2.4.1.41
- UniProt
- Q8MRC9
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) | protein | 504 | 31% helix, 25% strand | Q8MRC9 |
| B | Polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) | protein | 495 | 31% helix, 24% strand | Q8MRC9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.79 | 0.86 | 46 | empty |
| 2 | 964 | 0.75 | 0.77 | 77 | GOL |
| 3 | 581 | 0.65 | 0.76 | 62 | GOL, EDO |
| 4 | 424 | 0.60 | 0.76 | 34 | empty |
| 5 | 142 | 0.49 | 0.78 | 26 | EDO |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6E4R · Crystal Structure of the Drosophila Melanogaster Polypeptide N-Acetylgalactosaminyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8MRC9 · AlphaFold monomer V2.0 prediction for putative polypeptide… · a predicted model of the same protein · chain B 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 Q8MRC9
- Elsewhere: RCSB PDB 6E4R · PDBe 6E4R · UniProt Q8MRC9
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