Research workbench
Ternary complex of DNA polymerase beta with a gapped DNA containing (SYN)8ODG:DA at primer terminus and DG:DCMP(CF2)PPIN the active site
Analyse Ternary complex of DNA polymerase beta with a gapped DNA containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RJH
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG) P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 6CF, MG, NA, CL
- Pockets
- 3 · best druggability 0.71
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 | 326 | 50% helix, 14% strand | P06746 |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG) P*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*A)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- 6CF · 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.71 | 0.76 | 57 | 6CF, MG |
| 2 | 334 | 0.63 | 0.79 | 29 | empty |
| 3 | 212 | 0.58 | 0.80 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–T · 739 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 476 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–P · 392 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 388 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–D · 233 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3RJH · Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG:dA at… · 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 0.94
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 3RJH · PDBe 3RJH · UniProt P06746
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