MolNFT v1 · #32406 · protein + DNA
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddctp
2BPG: “Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddctp”. X-ray diffraction, 2 ligands (DCT, MG), 9 pockets (best druggability 0.59). MolNFT v1 #32406 on GenesisL1: 3D structure, binding sites…
- PDB
- 2BPG
- Type
- protein + DNA
- Length
- 678 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3'); DNA…
- UniProt
- P06766
- Ligands
- DCT, MG
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase beta | protein | 324 | 49% helix, 13% strand | P06766 |
| T, C | DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3') | dna | 8 | — | — |
| P, D | DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 2 copies · chains A, T, P, B, C, D
- MG · Magnesium ion · metal · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.59 | 0.79 | 26 | empty |
| 2 | 294 | 0.58 | 0.78 | 39 | DCT |
| 3 | 209 | 0.57 | 0.80 | 26 | empty |
| 4 | 197 | 0.53 | 0.79 | 18 | DCT |
| 5 | 104 | 0.42 | 0.78 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–C · 620 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–T · 582 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 384 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 377 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 344 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 2BPG · Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and… · the same entry in another collection · chain B against B, TM-score 1.00
- P06766 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06766) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P06766
- Elsewhere: RCSB PDB 2BPG · PDBe 2BPG · UniProt P06766
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