Research workbench
Human gpt (DPAGT1) H129 variant in complex with tunicamycin
Analyse Human gpt (DPAGT1) H129 variant in complex with tunicamycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BW6
- Type
- protein
- Length
- 1,476 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 0.75
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 368 | 67% helix, 7% strand | Q9H3H5 |
| B | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 374 | 65% helix, 6% strand | Q9H3H5 |
| C | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 365 | 67% helix, 4% strand | Q9H3H5 |
| D | Udp-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase (EC 2.7.8.15) | protein | 369 | 66% helix, 5% 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.75 | 0.78 | 82 | TUM |
| 2 | 619 | 0.74 | 0.81 | 52 | TUM |
| 3 | 635 | 0.73 | 0.80 | 55 | TUM |
| 4 | 217 | 0.72 | 0.87 | 28 | PGW |
| 5 | 589 | 0.72 | 0.80 | 55 | TUM |
Interfaces
5 interfaces between chains.
- C–D · 1836 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1807 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 421 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 371 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BW6 · Human GPT (DPAGT1) H129 variant in complex with tunicamycin · the same entry in another collection · chain D against D, TM-score 1.00
- Q9H3H5 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- dolichyl-phosphate… · a predicted model of the same protein · chain C 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 6BW6 · PDBe 6BW6 · UniProt Q9H3H5
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