MolNFT v1 · #47695 · protein + DNA
Human DNA polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA
2P66 · DNA (5'- D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “Human DNA polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA”. X-ray diffraction, 2 ligands (NA, PO4), 2 pockets (best druggability 0.72).…
- PDB
- 2P66
- Type
- protein + DNA
- Length
- 359 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- NA, PO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | dna | 16 | — | — |
| C | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') | dna | 11 | — | — |
| D | DNA (5'-D(P*(3DR)P*GP*TP*CP*GP*G)-3') | dna | 6 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 49% helix, 12% strand | P06746 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.72 | 0.76 | 79 | NA, PO4 |
| 2 | 212 | 0.60 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 522 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- C–A · 501 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 406 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–A · 389 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 229 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2P66 · Human DNA Polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P06746
- Elsewhere: RCSB PDB 2P66 · PDBe 2P66 · UniProt P06746
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