Research workbench
Binary complex of human DNA polymerase beta with an abasic site (thf) in the gapped DNA
Analyse Binary complex of human DNA polymerase beta with an abasic site (thf) in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ISC
- Type
- protein + DNA
- Length
- 358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; 5'-D(P*GP*TP*CP*GP*G)-3'; 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- NA
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 327 | 52% helix, 13% strand | P06746 |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3' | dna | 10 | — | — |
| T | 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3' | dna | 16 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 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 | 250 | 0.64 | 0.82 | 27 | empty |
| 2 | 444 | 0.62 | 0.77 | 40 | empty |
| 3 | 329 | 0.54 | 0.75 | 33 | NA |
| 4 | 101 | 0.36 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- P–T · 457 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–D · 382 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–T · 372 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–P · 326 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–T · 232 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3ISC · Binary complex of human DNA polymerase beta with an abasic site (THF) in the gapped DNA · 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 0.93
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 3ISC · PDBe 3ISC · UniProt P06746
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