Research workbench
Structure of human DNA polymerase beta complexed with a nicked DNA containing a 8BRG-C at N-1 position and G-C at N position
Analyse Structure of human DNA polymerase beta complexed with a nicked DNA containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NM1
- Type
- protein + DNA
- Length
- 358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*GP*AP*CP*GP*(BGM)P*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- MG, NA, PO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*CP*CP*GP*AP*CP*GP*(BGM)P*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3' | dna | 11 | — | — |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 50% helix, 13% strand | P06746 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains P, A
- NA · Sodium ion · metal · 2 copies · chains D, A, P
- PO4 · Phosphate ion · ion · chains P, 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 | 880 | 0.70 | 0.76 | 60 | PO4, MG |
| 2 | 335 | 0.61 | 0.78 | 28 | empty |
| 3 | 205 | 0.57 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- T–A · 731 Ų buried · 15 hydrogen bonds · protein-nucleic
- P–A · 533 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 508 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- D–A · 389 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 232 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4NM1 · Structure of human DNA polymerase beta complexed with a nicked DNA containing a 8BrG-C at… · 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 4NM1 · PDBe 4NM1 · UniProt P06746
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