Research workbench
The mouse pngase-HR23 complex reveals a complete remodulation of the protein-protein interface compared to its yeast orthologs
Analyse The mouse pngase-HR23 complex reveals a complete remodulation of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F4O
- Type
- protein
- Length
- 354 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide N-glycanase; Xp-C repair complementing complex 58 kda protein; Phq-val-ala-asp-CF0
- EC
- 3.5.1.52
- UniProt
- P54728
- Ligands
- PHQ, ZN, CF0, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide N-glycanase (EC 3.5.1.52) | protein | 290 | 43% helix, 20% strand | — |
| B | Xp-C repair complementing complex 58 kda protein | protein | 61 | 74% helix, 0% strand | P54728 |
| I | Phq-val-ala-asp-CF0 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains A, I
- ZN · Zinc ion · metal · 2 copies · chains A
- CF0 · Fluoromethane · ion · chains A, I
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.72 | 0.87 | 29 | empty |
| 2 | 96 | 0.45 | 0.80 | 21 | empty |
| 3 | 112 | 0.41 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 891 Ų buried · 8 hydrogen bonds · protein-protein
- A–I · 324 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2F4O · The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of the Protein-Protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P54728 · AlphaFold monomer V2.0 prediction for UV excision repair protein RAD23 homolog B (P54728) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 P54728
- Elsewhere: RCSB PDB 2F4O · PDBe 2F4O · UniProt P54728
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