MolNFT v1 · #144520 · protein
Human gpt (DPAGT1) in complex with tunicamycin
6BW5 · Udp-N-acetylglucosamine--dolichyl-phosphate N…: “Human gpt (DPAGT1) in complex with tunicamycin”. X-ray diffraction, 2 ligands (TUM, PGW), 20 pockets (best druggability 0.79). MolNFT v1 #144520 on GenesisL1: 3D structure, binding…
- PDB
- 6BW5
- Type
- protein
- Length
- 1,484 residues
- Chains
- 4
- 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
- TUM, PGW
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 65% 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 | 378 | 64% helix, 7% strand | Q9H3H5 |
| B | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 369 | 65% helix, 7% strand | Q9H3H5 |
| C | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 375 | 65% helix, 8% strand | Q9H3H5 |
| D | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 362 | 67% helix, 6% strand | Q9H3H5 |
Ligands and binding sites
- TUM · Tunicamycin · ligand · 4 copies · chains A, B, C, D
- PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 4 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.79 | 0.81 | 97 | TUM |
| 2 | 841 | 0.74 | 0.78 | 70 | TUM |
| 3 | 233 | 0.74 | 0.87 | 28 | PGW |
| 4 | 239 | 0.73 | 0.87 | 30 | PGW |
| 5 | 251 | 0.73 | 0.86 | 32 | PGW |
Interfaces
5 interfaces between chains.
- C–D · 1759 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1716 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 406 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 357 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 Q9H3H5
- Elsewhere: RCSB PDB 6BW5 · PDBe 6BW5 · UniProt Q9H3H5
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