MolNFT v1 · #11723 · protein
Crystal structure of human AGX1 complexed with udpgalnac
1JV3 · GLCNAC1P uridyltransferase isoform 1: AGX1: “Crystal structure of human AGX1 complexed with udpgalnac”. X-ray diffraction, 1 ligand (UD2), 15 pockets (best druggability 0.85). MolNFT v1 #11723 on GenesisL1: 3D structure, binding…
- PDB
- 1JV3
- Type
- protein
- Length
- 974 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLCNAC1P uridyltransferase isoform 1: AGX1
- EC
- 2.7.7.-
- UniProt
- Q16222
- Ligands
- UD2
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLCNAC1P uridyltransferase isoform 1: AGX1 (EC 2.7.7.-) | protein | 490 | 37% helix, 22% strand | Q16222 |
| B | GLCNAC1P uridyltransferase isoform 1: AGX1 (EC 2.7.7.-) | protein | 484 | 36% helix, 22% 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.85 | 0.93 | 62 | UD2 |
| 2 | 425 | 0.84 | 0.92 | 69 | empty |
| 3 | 495 | 0.84 | 0.91 | 70 | UD2 |
| 4 | 649 | 0.70 | 0.78 | 61 | empty |
| 5 | 493 | 0.69 | 0.79 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 2688 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1JV3 · Crystal structure of human AGX1 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 B against A, TM-score 1.00
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 1JV3 · PDBe 1JV3 · UniProt Q16222
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