MolNFT v1 · #141764 · protein
Crystal structure of human gnt-V luminal domain in apo form
5ZIB · Alpha-1,6-mannosylglycoprotein 6-beta-N…: “Crystal structure of human gnt-V luminal domain in apo form”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.72). MolNFT v1 #141764 on GenesisL1: 3D structure, binding…
- PDB
- 5ZIB
- Type
- protein
- Length
- 579 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannosylglycoprotein 6-beta-N- acetylglucosaminyltransferase a
- EC
- 2.4.1.155
- UniProt
- Q09328
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannosylglycoprotein 6-beta-N- acetylglucosaminyltransferase a (EC 2.4.1.155) | protein | 579 | 39% helix, 15% strand | Q09328 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.72 | 0.98 | 25 | empty |
| 2 | 629 | 0.69 | 0.77 | 65 | empty |
| 3 | 275 | 0.63 | 0.80 | 45 | empty |
| 4 | 313 | 0.61 | 0.79 | 33 | empty |
| 5 | 118 | 0.39 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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 Q09328
- Elsewhere: RCSB PDB 5ZIB · PDBe 5ZIB · UniProt Q09328
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