MolNFT v1 · #106128 · protein + DNA
Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8- dihydro-GUANINE(8-oxog) and dctp soaked with MGCL2 for 30 S
4RPY: “Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8- dihydro-GUANINE(8-oxog) and dctp soaked…”. X-ray diffraction, 5 ligands (DCP, PPV, NA), 2 pockets (best druggability 0.75). MolNFT v1 #106128 on GenesisL1: 3D…
- PDB
- 4RPY
- Type
- protein + DNA
- Length
- 358 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
- DCP, PPV, NA, MG, CL
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 52% helix, 13% 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*C)-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
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, P, T, D
- PPV · Pyrophosphate · ligand · chains A, P
- NA · Sodium ion · metal · 7 copies · chains A, D, P, T
- MG · Magnesium ion · metal · 3 copies · chains A, P
- CL · Chloride ion · ion · 4 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A, T, P
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 | 969 | 0.75 | 0.78 | 74 | MG, ACT, PPV |
| 2 | 217 | 0.54 | 0.78 | 25 | CL |
Interfaces
5 interfaces between chains.
- A–T · 711 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 526 Ų buried · 18 hydrogen bonds · protein-nucleic
- P–T · 500 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–D · 380 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–T · 197 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 4RPY · 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 4RPY · PDBe 4RPY · UniProt P06746
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