Research workbench
Human ogt in complex with udp and fused substrate peptide (TAB1)
Analyse Human ogt in complex with udp and fused substrate peptide (TAB1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LVV
- Type
- protein
- Length
- 720 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda SUBUNIT,UDP-N…
- EC
- 2.4.1.255
- UniProt
- O15294
- Ligands
- UDP, NAG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda SUBUNIT,UDP-N- acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 720 | 50% helix, 12% strand | O15294 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.80 | 0.82 | 99 | NAG |
| 2 | 301 | 0.80 | 0.91 | 54 | UDP, NAG |
| 3 | 54 | 0.70 | 0.97 | 16 | empty |
| 4 | 286 | 0.60 | 0.79 | 33 | empty |
| 5 | 105 | 0.36 | 0.74 | 20 | empty |
Modifications
Observed in the structure: 3 glycan (O-glycosylation).
Compared structures
- 5LVV · Human OGT in complex with UDP and fused substrate peptide (Tab1) · 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
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 5LVV · PDBe 5LVV · UniProt O15294
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