MolNFT v1 · #106138 · protein + DNA
Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8- dihydro-GUANINE(8-oxog) and datp soaked with MNCL2 for 35 S
4RQ8: “Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8- dihydro-GUANINE(8-oxog) and datp soaked…”. X-ray diffraction, 4 ligands (PPV, NA, MN), 5 pockets (best druggability 0.70). MolNFT v1 #106138 on GenesisL1: 3D…
- PDB
- 4RQ8
- Type
- protein + DNA
- Length
- 365 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(P*GP*TP*CP*GP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- PPV, NA, MN, CL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 333 | 50% helix, 14% strand | P06746 |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*A)-3') | dna | 11 | — | — |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A, P
- NA · Sodium ion · metal · 9 copies · chains A, D, P, T
- MN · Manganese (II) ion · metal · 6 copies · chains A, P
- CL · Chloride ion · ion · 6 copies · chains A, T
- ACT · Acetate ion · additive · 6 copies · chains A, D, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.70 | 0.78 | 55 | PPV, MN, NA |
| 2 | 191 | 0.53 | 0.78 | 22 | empty |
| 3 | 121 | 0.51 | 0.82 | 18 | CL, ACT |
| 4 | 54 | 0.32 | 0.77 | 13 | CL |
| 5 | 50 | 0.28 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–T · 690 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–P · 560 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 513 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–D · 373 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–T · 191 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4RQ8 · Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG)… · the same entry in another collection · chain A against A, 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 0.92
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 4RQ8 · PDBe 4RQ8 · UniProt P06746
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