MolNFT v1 · #128424 · protein
The human O-glcnac transferase in complex with a bisubstrate inhibitor
5NPS · Udp-N-acetylglucosamine--peptide N…: “The human O-glcnac transferase in complex with a bisubstrate inhibitor”. X-ray diffraction, 2 ligands (94T, NH2), 7 pockets (best druggability 0.79). MolNFT v1 #128424 on GenesisL1: 3D…
- PDB
- 5NPS
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit…
- EC
- 2.4.1.255
- UniProt
- O15294
- Ligands
- 94T, NH2
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 693 | 52% helix, 13% strand | O15294 |
| D | 5,6-dihydro-BENZO[H]CINNOLIN-3-ylamine | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- 94T · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene) pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] propyl hydrogen phosphate · ligand · chains A, D
- NH2 · Amino group · ion · chains A, D
- ACY · Acetic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.79 | 0.91 | 42 | 94T |
| 2 | 1056 | 0.74 | 0.77 | 88 | empty |
| 3 | 56 | 0.71 | 0.97 | 18 | empty |
| 4 | 165 | 0.52 | 0.79 | 25 | empty |
| 5 | 113 | 0.38 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–D · 441 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct, covalent ligand).
Compared structures
- 5NPS · The human O-GlcNAc transferase in complex with a bisubstrate inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- O15294 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O15294
- Elsewhere: RCSB PDB 5NPS · PDBe 5NPS · UniProt O15294
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