MolNFT v1 · #11733 · protein
Crystal structure of human AGX2 complexed with udpglcnac
1JVD · Udpglcnac pyrophosphorylase (AGX2): “Crystal structure of human AGX2 complexed with udpglcnac”. X-ray diffraction, 1 ligand (UD1), 13 pockets (best druggability 0.87). MolNFT v1 #11733 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1JVD
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udpglcnac pyrophosphorylase (AGX2)
- EC
- 2.7.7.23
- UniProt
- Q16222
- Ligands
- UD1
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udpglcnac pyrophosphorylase (AGX2) (EC 2.7.7.23) | protein | 480 | 38% helix, 23% strand | Q16222 |
| B | Udpglcnac pyrophosphorylase (AGX2) (EC 2.7.7.23) | protein | 486 | 39% helix, 23% strand | Q16222 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.87 | 0.89 | 127 | empty |
| 2 | 552 | 0.81 | 0.87 | 64 | UD1 |
| 3 | 347 | 0.72 | 0.84 | 44 | UD1 |
| 4 | 663 | 0.68 | 0.76 | 59 | empty |
| 5 | 310 | 0.62 | 0.79 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 2368 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1JVD · Crystal structure of human AGX2 complexed with udpglcnac · 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 1JVD · PDBe 1JVD · UniProt Q16222
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