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Complex structure of PCNA with UHRF2
Analyse Complex structure of PCNA with UHRF2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YCO
- Type
- protein
- Length
- 1,014 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; E3 ubiquitin-protein ligase UHRF2
- EC
- 2.3.2.27
- UniProt
- P12004, Q96PU4
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Proliferating cell nuclear antigen | protein | 250 | 18% helix, 47% strand | P12004 |
| C | Proliferating cell nuclear antigen | protein | 248 | 18% helix, 47% strand | P12004 |
| E, F | E3 ubiquitin-protein ligase UHRF2 (EC 2.3.2.27) | protein | 8 | 0% helix, 0% strand | Q96PU4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.69 | 0.84 | 39 | empty |
| 2 | 269 | 0.61 | 0.80 | 32 | empty |
| 3 | 91 | 0.43 | 0.79 | 18 | empty |
| 4 | 101 | 0.39 | 0.76 | 17 | empty |
| 5 | 56 | 0.32 | 0.76 | 13 | empty |
Interfaces
7 interfaces between chains.
- A–D · 756 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 747 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 737 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 543 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 541 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P12004
- Every structure of UniProt Q96PU4
- Elsewhere: RCSB PDB 5YCO · PDBe 5YCO · UniProt P12004 · UniProt Q96PU4
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