MolNFT v1 · #11735 · protein
Crystal structure of human AGX2 complexed with udpgalnac
1JVG · GLCNAC1P uridyltransferase: “Crystal structure of human AGX2 complexed with udpgalnac”. X-ray diffraction, 1 ligand (UD2), 17 pockets (best druggability 0.86). MolNFT v1 #11735 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1JVG
- Type
- protein
- Length
- 965 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLCNAC1P uridyltransferase
- EC
- 2.7.7.23
- UniProt
- Q16222
- Ligands
- UD2
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLCNAC1P uridyltransferase (EC 2.7.7.23) | protein | 485 | 38% helix, 22% strand | Q16222 |
| B | GLCNAC1P uridyltransferase (EC 2.7.7.23) | protein | 480 | 38% helix, 23% strand | Q16222 |
Ligands and binding sites
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.86 | 0.90 | 89 | empty |
| 2 | 210 | 0.74 | 0.90 | 34 | UD2 |
| 3 | 285 | 0.74 | 0.87 | 44 | UD2 |
| 4 | 89 | 0.64 | 0.90 | 30 | empty |
| 5 | 72 | 0.59 | 0.89 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2176 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1JVG · Crystal structure of human AGX2 complexed with udpgalnac · the same entry in another collection · chain A against A, TM-score 1.00
- Q16222 · AlphaFold monomer V2.0 prediction for udp-N-acetylhexosamine pyrophosphorylase (Q16222) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q16222
- Elsewhere: RCSB PDB 1JVG · PDBe 1JVG · UniProt Q16222
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