Research workbench
Crystal structure of human O-glcnac transferase in complex with udp and a glycopeptide
Analyse Crystal structure of human O-glcnac transferase in complex with udp and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GYW
- Type
- protein
- Length
- 1,397 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit; Casein…
- EC
- 2.4.1.255, 2.7.11.1
- UniProt
- O15294, P68400
- Ligands
- UDP, NAG, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 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 | 695 | 52% helix, 13% strand | O15294 |
| B, D | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 14 | 0% helix, 7% strand | P68400 |
| C | Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 674 | 51% helix, 13% strand | O15294 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.81 | 0.94 | 48 | UDP, NAG |
| 2 | 281 | 0.80 | 0.92 | 64 | UDP, NAG |
| 3 | 1070 | 0.76 | 0.79 | 87 | empty |
| 4 | 845 | 0.75 | 0.79 | 91 | SO4 |
| 5 | 772 | 0.74 | 0.79 | 71 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 969 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 793 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (O-glycosylation).
Compared structures
- 4GYW · Crystal structure of human O-GlcNAc Transferase in complex with UDP and a glycopeptide · the same entry in another collection · chain D against D, TM-score 1.00
- O15294 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain C against A, TM-score 0.99
- P68400 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P68400) · a predicted model of the same protein · chain B against A, TM-score 0.24
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
- Every structure of UniProt P68400
- Elsewhere: RCSB PDB 4GYW · PDBe 4GYW · UniProt O15294 · UniProt P68400
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