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Structure of human DNA polymerase beta complexed with 8-brg as the template base in a 1-nucleotide gapped DNA
Analyse Structure of human DNA polymerase beta complexed with 8-brg as the template… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M2Y
- Type
- protein + DNA
- Length
- 350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; Template DNA strand; Up-primer; Down-primer
- 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 · 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 | 319 | 52% helix, 13% strand | P06746 |
| T | Template DNA strand | dna | 16 | — | — |
| P | Up-primer | dna | 10 | — | — |
| D | Down-primer | 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 | 260 | 0.63 | 0.82 | 27 | empty |
| 2 | 394 | 0.63 | 0.78 | 42 | empty |
| 3 | 415 | 0.58 | 0.75 | 38 | empty |
| 4 | 110 | 0.36 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- T–P · 474 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–T · 422 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 386 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–P · 325 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 228 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4M2Y · Structure of human DNA polymerase beta complexed with 8-BrG as the template base in a… · the same entry in another collection · chain T against T, 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 4M2Y · PDBe 4M2Y · UniProt P06746
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