Research workbench
Structure of an archaeal PCNA1-PCNA2-FEN1 complex
Analyse Structure of an archaeal PCNA1-PCNA2-FEN1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IZO
- Type
- protein
- Length
- 756 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flap structure-specific endonuclease; DNA polymerase sliding clamp C; DNA polymerase…
- EC
- 3.1.-.-
- UniProt
- Q980U8, Q97Z84, P57766
- Ligands
- ZN, MG
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flap structure-specific endonuclease (EC 3.1.-.-) | protein | 268 | 48% helix, 12% strand | Q980U8 |
| B | DNA polymerase sliding clamp C | protein | 244 | 19% helix, 48% strand | Q97Z84 |
| C | DNA polymerase sliding clamp B | protein | 244 | 19% helix, 47% strand | P57766 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.48 | 0.76 | 34 | empty |
| 2 | 92 | 0.48 | 0.81 | 14 | empty |
| 3 | 65 | 0.33 | 0.76 | 16 | MG |
| 4 | 76 | 0.30 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 903 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 674 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2IZO · Structure of an Archaeal PCNA1-PCNA2-FEN1 Complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q97Z84 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 2 (Q97Z84) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P57766 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 1 (P57766) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q980U8 · AlphaFold monomer V2.0 prediction for flap endonuclease 1 (Q980U8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q980U8
- Every structure of UniProt Q97Z84
- Every structure of UniProt P57766
- Elsewhere: RCSB PDB 2IZO · PDBe 2IZO · UniProt Q980U8 · UniProt Q97Z84 · UniProt P57766
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