MolNFT v1 · #74826 · protein
Structure of the PCNA:RNASE hii complex from archaeoglobus fulgidus.
3P83 · DNA polymerase sliding clamp: “Structure of the PCNA:RNASE hii complex from archaeoglobus fulgidus.”. X-ray diffraction, 11 pockets (best druggability 0.74). MolNFT v1 #74826 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3P83
- Type
- protein
- Length
- 1,351 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp; Ribonuclease hii
- EC
- 3.1.26.4
- UniProt
- O29912, O29634
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase sliding clamp | protein | 244 | 19% helix, 46% strand | O29912 |
| C | DNA polymerase sliding clamp | protein | 243 | 19% helix, 47% strand | O29912 |
| D | Ribonuclease hii (EC 3.1.26.4) | protein | 213 | 51% helix, 18% strand | O29634 |
| E | Ribonuclease hii (EC 3.1.26.4) | protein | 202 | 49% helix, 18% strand | O29634 |
| F | Ribonuclease hii (EC 3.1.26.4) | protein | 205 | 51% helix, 18% strand | O29634 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.74 | 0.79 | 68 | empty |
| 2 | 790 | 0.72 | 0.78 | 69 | empty |
| 3 | 329 | 0.68 | 0.82 | 52 | empty |
| 4 | 339 | 0.56 | 0.75 | 42 | empty |
| 5 | 210 | 0.48 | 0.75 | 27 | empty |
Interfaces
10 interfaces between chains.
- A–D · 751 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 744 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 697 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 622 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3P83 · Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus. · the same entry in another collection · chain F against F, TM-score 1.00
- O29912 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp (O29912) · a predicted model of the same protein · chain C against A, TM-score 0.99
- O29634 · AlphaFold monomer V2.0 prediction for ribonuclease hii (O29634) · a predicted model of the same protein · chain F against A, TM-score 0.94
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 O29912
- Every structure of UniProt O29634
- Elsewhere: RCSB PDB 3P83 · PDBe 3P83 · UniProt O29912 · UniProt O29634
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.