MolNFT v1 · #39905 · protein + DNA
DNA polymerase beta with a BENZO[C]PHENANTHRENE diol epoxide adducted guanine base
2I9G · 5'-D(P*GP*TP*CP*GP*G)-3': “DNA polymerase beta with a BENZO[C]PHENANTHRENE diol epoxide adducted guanine base”. X-ray diffraction, 3 ligands (BPI, NA, CL), 3 pockets (best druggability 0.73). MolNFT v1 #39905 on GenesisL1: 3D…
- PDB
- 2I9G
- Type
- protein + DNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*GP*TP*CP*GP*G)-3'; 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'; 5'…
- EC
- 2.7.7.7
- UniProt
- P06746
- Ligands
- BPI, NA, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3' | dna | 10 | — | — |
| T | 5'- D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' | dna | 16 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7) | protein | 325 | 51% helix, 13% strand | P06746 |
Ligands and binding sites
- BPI · (1S)-1,2,3,4-tetrahydro-benzo[c]phenanthrene-2,3,4-triol · ligand · chains P, T, A
- NA · Sodium ion · metal · 2 copies · chains P, A, D
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.73 | 0.77 | 86 | BPI |
| 2 | 208 | 0.62 | 0.83 | 25 | empty |
| 3 | 56 | 0.31 | 0.75 | 12 | empty |
Interfaces
5 interfaces between chains.
- T–A · 511 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 460 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- D–A · 385 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–A · 323 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–T · 229 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 2I9G · DNA Polymerase Beta with a Benzo[c]phenanthrene diol epoxide adducted guanine base · the same entry in another collection · chain D against D, 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 2I9G · PDBe 2I9G · UniProt P06746
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