MolNFT v1 · #26910 · protein
Structure of a PEPTIDE:N-glycanase-RAD23 complex
1X3W: “Structure of a PEPTIDE:N-glycanase-RAD23 complex”. X-ray diffraction, 3 ligands (GLC, FRU, ZN), 5 pockets (best druggability 0.71). MolNFT v1 #26910 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1X3W
- Type
- protein
- Length
- 377 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PEPTIDE:N-glycanase; UV excision repair protein RAD23
- EC
- 3.5.1.52
- UniProt
- Q02890, P32628
- Ligands
- GLC, FRU, ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PEPTIDE:N-glycanase (EC 3.5.1.52) | protein | 320 | 45% helix, 19% strand | Q02890 |
| B | UV excision repair protein RAD23 | protein | 57 | 79% helix, 0% strand | P32628 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
- FRU · beta-D-fructofuranose · sugar · 3 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.71 | 0.86 | 38 | empty |
| 2 | 68 | 0.39 | 0.79 | 15 | empty |
| 3 | 85 | 0.35 | 0.75 | 16 | GLC, FRU |
| 4 | 75 | 0.31 | 0.73 | 19 | empty |
| 5 | 50 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1159 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 1X3W · Structure of a peptide:N-glycanase-Rad23 complex · 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 0.98
- 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 0.70
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 1X3W · PDBe 1X3W · UniProt Q02890 · UniProt P32628
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