MolNFT v1 · #136710 · protein + DNA
DNA polymerase beta open product complex with 8-OXOG:C and inserted dctp
5V1J: “DNA polymerase beta open product complex with 8-OXOG:C and inserted dctp”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.63). MolNFT v1 #136710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V1J
- Type
- protein + DNA
- Length
- 351 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*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- NA
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 319 | 50% helix, 13% strand | P06746 |
| 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 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, P, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.63 | 0.84 | 24 | empty |
| 2 | 491 | 0.60 | 0.75 | 46 | empty |
| 3 | 203 | 0.59 | 0.81 | 26 | empty |
| 4 | 112 | 0.34 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- T–P · 502 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–P · 461 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–T · 428 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 371 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 229 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5V1J · DNA polymerase beta open product complex with 8-oxoG:C and inserted dCTP · 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 5V1J · PDBe 5V1J · UniProt P06746
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