Research workbench
Crystal structure of PCNA3 monomer from sulfolobus solfataricus.
Analyse Crystal structure of PCNA3 monomer from sulfolobus solfataricus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IJX
- Type
- protein
- Length
- 976 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp a
- UniProt
- P57765
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA polymerase sliding clamp a | protein | 244 | 21% helix, 46% strand | P57765 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.85 | 0.89 | 90 | empty |
| 2 | 198 | 0.76 | 0.91 | 30 | empty |
| 3 | 56 | 0.74 | 0.99 | 21 | empty |
| 4 | 465 | 0.68 | 0.80 | 53 | EDO |
| 5 | 183 | 0.63 | 0.84 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 803 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 677 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 609 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 150 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2IJX · Crystal structure of PCNA3 monomer from Sulfolobus solfataricus. · the same entry in another collection · chain A against A, TM-score 1.00
- P57765 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 3 (P57765) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P57765
- Elsewhere: RCSB PDB 2IJX · PDBe 2IJX · UniProt P57765
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