MolNFT v1 · #57270 · protein
Crystal structure of pyrococcus furiosus DNA POLYMERASE/PCNA monomer mutant complex
3A2F: “Crystal structure of pyrococcus furiosus DNA POLYMERASE/PCNA monomer mutant complex”. X-ray diffraction, 12 pockets (best druggability 0.77). MolNFT v1 #57270 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A2F
- Type
- protein
- Length
- 1,020 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA polymerase sliding clamp
- EC
- 2.7.7.7
- UniProt
- P61875, O73947
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 773 | 39% helix, 21% strand | P61875 |
| B | DNA polymerase sliding clamp | protein | 247 | 17% helix, 48% strand | O73947 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.77 | 0.99 | 19 | empty |
| 2 | 440 | 0.67 | 0.79 | 53 | empty |
| 3 | 398 | 0.65 | 0.79 | 29 | empty |
| 4 | 248 | 0.57 | 0.78 | 21 | empty |
| 5 | 294 | 0.54 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3A2F · Crystal Structure of Pyrococcus furiosus DNA polymerase/PCNA monomer mutant complex · the same entry in another collection · chain B against B, TM-score 1.00
- O73947 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp (O73947) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P61875 · AlphaFold monomer V2.0 prediction for DNA polymerase (P61875) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P61875
- Every structure of UniProt O73947
- Elsewhere: RCSB PDB 3A2F · PDBe 3A2F · UniProt P61875 · UniProt O73947
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