Research workbench
Human ogt in complex with udp and fused substrate peptide (HCF1)
Analyse Human ogt in complex with udp and fused substrate peptide (HCF1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LWV
- Type
- protein
- Length
- 711 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Host cell factor 1,UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110…
- EC
- 2.4.1.255
- UniProt
- P51610, O15294
- Ligands
- UDP, PO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Host cell factor 1,UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 711 | 51% helix, 12% strand | P51610, O15294 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.80 | 0.82 | 78 | PO4 |
| 2 | 640 | 0.77 | 0.82 | 67 | UDP |
| 3 | 67 | 0.73 | 0.98 | 18 | empty |
| 4 | 191 | 0.51 | 0.77 | 28 | empty |
| 5 | 144 | 0.41 | 0.74 | 21 | empty |
Compared structures
- 5LWV · Human OGT in complex with UDP and fused substrate peptide (HCF1) · 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 0.94
- P51610 · AlphaFold monomer V2.0 prediction for host cell factor 1 (P51610) · a predicted model of the same protein · chain A against A, TM-score 0.23
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 P51610
- Every structure of UniProt O15294
- Elsewhere: RCSB PDB 5LWV · PDBe 5LWV · UniProt P51610 · UniProt O15294
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