MolNFT v1 · #62887 · protein
Complex of yeast pngase with GLCNAC2-iac.
3ESW · Peptide-N(4)-(N-acetyl-beta-GLUCOSAMINYL)ASPARAGINE amidase: “Complex of yeast pngase with GLCNAC2-iac.”. X-ray diffraction, 2 ligands (NAG, ZN), 4 pockets (best druggability 0.71). MolNFT v1 #62887 on GenesisL1: 3D structure…
- PDB
- 3ESW
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide-N(4)-(N-acetyl-beta-GLUCOSAMINYL)ASPARAGINE amidase; UV excision repair protein…
- EC
- 3.5.1.52
- UniProt
- Q02890, P32628
- Ligands
- NAG, ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide-N(4)-(N-acetyl-beta-GLUCOSAMINYL)ASPARAGINE amidase (EC 3.5.1.52) | protein | 333 | 47% helix, 18% strand | Q02890 |
| B | UV excision repair protein RAD23 | protein | 55 | 75% helix, 0% strand | P32628 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.71 | 0.83 | 43 | empty |
| 2 | 172 | 0.43 | 0.74 | 22 | empty |
| 3 | 94 | 0.40 | 0.77 | 18 | empty |
| 4 | 64 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1085 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan, 1 modified (glycosylation, alkylation).
Compared structures
- 3ESW · Complex of yeast PNGase with GlcNAc2-IAc. · the same entry in another collection · chain A against A, TM-score 1.00
- Q02890 · AlphaFold monomer V2.0 prediction for peptide-N(4)-(N-acetyl-beta… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P32628 · AlphaFold monomer V2.0 prediction for UV excision repair protein RAD23 (P32628) · a predicted model of the same protein · chain B against A, TM-score 0.69
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 Q02890
- Every structure of UniProt P32628
- Elsewhere: RCSB PDB 3ESW · PDBe 3ESW · UniProt Q02890 · UniProt P32628
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