MolNFT v1 · #136718 · protein + DNA
DNA polymerase beta reactant complex with 8-OXOG:C at the primer terminus and incoming dctp
5V1R · DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “DNA polymerase beta reactant complex with 8-OXOG:C at the primer terminus and incoming dctp”. X-ray diffraction, 5 ligands (DCP, PPV, MG), 2 pockets (best druggability…
- PDB
- 5V1R
- Type
- protein + DNA
- Length
- 358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- DCP, PPV, MG, NA, CL
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG)P*C)-3') | dna | 11 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 52% helix, 13% strand | P06746 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains T, P, A
- PPV · Pyrophosphate · ligand · chains P, A
- MG · Magnesium ion · metal · 3 copies · chains P, A
- NA · Sodium ion · metal · 2 copies · chains P, A, D
- CL · Chloride ion · ion · 4 copies · chains A
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 | 1016 | 0.76 | 0.79 | 73 | MG, PPV |
| 2 | 181 | 0.55 | 0.80 | 24 | empty |
Interfaces
5 interfaces between chains.
- T–A · 717 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–A · 550 Ų buried · 19 hydrogen bonds · protein-nucleic
- T–P · 505 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- D–A · 360 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 232 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 5V1R · DNA polymerase beta reactant complex with 8-oxoG:C at the primer terminus and incoming… · the same entry in another collection · chain T against T, 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 0.94
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 5V1R · PDBe 5V1R · UniProt P06746
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