Research workbench
Crystal structure of the drosophila melanogaster polypeptide N- acetylgalactosaminyl transferase PGANT9A in complex with udp and MN2+
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
- 6E4Q
- Type
- protein
- Length
- 2,013 residues
- Chains
- 4
- 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
- UDP, NAG, MN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) | protein | 505 | 30% helix, 23% strand | Q8MRC9 |
| B, C | Polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) | protein | 503 | 29% helix, 23% strand | Q8MRC9 |
| D | Polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) | protein | 502 | 29% helix, 24% strand | Q8MRC9 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.73 | 0.79 | 64 | MN, UDP |
| 2 | 660 | 0.72 | 0.79 | 62 | UDP, EDO |
| 3 | 605 | 0.71 | 0.79 | 38 | UDP |
| 4 | 503 | 0.70 | 0.80 | 40 | UDP |
| 5 | 370 | 0.55 | 0.74 | 59 | empty |
Interfaces
3 interfaces between chains.
- A–B · 555 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 530 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6E4Q · Crystal Structure of the Drosophila Melanogaster Polypeptide N-Acetylgalactosaminyl… · the same entry in another collection · chain D against D, 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 0.99
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 6E4Q · PDBe 6E4Q · UniProt Q8MRC9
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