Research workbench
Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma- difluoromethylene triphosphate
Analyse Ternary complex of DNA polymerase beta with a dideoxy terminated primer and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ISO
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- Q3KP48
- Ligands
- GFF, NA, MG, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'- D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3' | dna | 10 | — | — |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| A | Polymerase (DNA directed), beta (EC 2.7.7.7) | protein | 326 | 51% helix, 13% strand | Q3KP48 |
Ligands and binding sites
- GFF · 2'-deoxy-5'-O-[({[difluoro(phosphono)methyl](hydroxy) phosphoryl}oxy)(hydroxy)phosphoryl]guanosine · ligand · chains T, P, A
- NA · Sodium ion · metal · 3 copies · chains P, A, D
- MG · Magnesium ion · metal · chains A
- 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 | 1025 | 0.71 | 0.75 | 63 | MG, GFF |
| 2 | 340 | 0.61 | 0.78 | 31 | empty |
| 3 | 219 | 0.56 | 0.79 | 27 | empty |
Interfaces
5 interfaces between chains.
- T–A · 696 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 466 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- D–A · 371 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–A · 356 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 230 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2ISO · Ternary complex of DNA Polymerase beta with a dideoxy terminated primer and… · the same entry in another collection · chain T against T, TM-score 1.00
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 Q3KP48
- Elsewhere: RCSB PDB 2ISO · PDBe 2ISO · UniProt Q3KP48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.