MolNFT v1 · #128935 · protein
Crystal structure of human udp-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with tunicamycin
5O5E · Udp-N-acetylglucosamine--dolichyl-phosphate N…: “Crystal structure of human udp-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase…”. X-ray diffraction, 3 ligands (P6L, 9LH, UNL), 3 pockets (best…
- PDB
- 5O5E
- Type
- protein
- Length
- 381 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase
- EC
- 2.7.8.15
- UniProt
- Q9H3H5
- Ligands
- P6L, 9LH, UNL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 381 | 63% helix, 7% strand | Q9H3H5 |
Ligands and binding sites
- P6L · (2S)-3-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6E)-hexadec-6-enoyloxy]propyl (8E)-octadec-8-enoate · ligand · chains A
- 9LH · Tunicamycin · ligand · chains A
- UNL · Unknown ligand · ligand · chains A
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 | 575 | 0.76 | 0.83 | 52 | 9LH |
| 2 | 92 | 0.42 | 0.78 | 14 | empty |
| 3 | 102 | 0.36 | 0.74 | 25 | empty |
Compared structures
- 5O5E · Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H3H5 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- dolichyl-phosphate… · a predicted model of the same protein · chain A 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 Q9H3H5
- Elsewhere: RCSB PDB 5O5E · PDBe 5O5E · UniProt Q9H3H5
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