MolNFT v1 · #171367 · protein
Crystal structure of human AGX1 mutant complexed with udpglcnac
6Z2F · Udp-N-acetylhexosamine pyrophosphorylase: “Crystal structure of human AGX1 mutant complexed with udpglcnac”. X-ray diffraction, 1 ligand (UD1), 14 pockets (best druggability 0.72). MolNFT v1 #171367 on GenesisL1: 3D structure…
- PDB
- 6Z2F
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylhexosamine pyrophosphorylase
- EC
- 2.7.7.83, 2.7.7.23
- UniProt
- Q16222
- Ligands
- UD1
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylhexosamine pyrophosphorylase (EC 2.7.7.83, 2.7.7.23) | protein | 469 | 38% helix, 22% strand | Q16222 |
| B | Udp-N-acetylhexosamine pyrophosphorylase (EC 2.7.7.83, 2.7.7.23) | protein | 475 | 38% 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
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.72 | 0.79 | 66 | UD1 |
| 2 | 669 | 0.70 | 0.78 | 60 | UD1 |
| 3 | 362 | 0.56 | 0.75 | 39 | empty |
| 4 | 144 | 0.50 | 0.79 | 30 | empty |
| 5 | 118 | 0.44 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 153 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (alkylation).
Compared structures
- 6Z2F · Crystal structure of human AGX1 mutant 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 6Z2F · PDBe 6Z2F · UniProt Q16222
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