MolNFT v1 · #101255 · protein + DNA
Structure of human DNA polymerase beta complexed with nicked DNA containing a template 8BRG and incoming CTP
4NLN: “Structure of human DNA polymerase beta complexed with nicked DNA containing a template 8BRG and incoming CTP”. X-ray diffraction, 3 ligands (MG, NA, PO4), 4 pockets (best druggability 0.67). MolNFT v1 #101255 on GenesisL1: 3D…
- PDB
- 4NLN
- 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(*CP*CP*GP*AP*CP*(BGM)P*TP*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
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 51% helix, 12% strand | P06746 |
| T | 5'-D(*CP*CP*GP*AP*CP*(BGM)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*AP*C)-3' | dna | 11 | — | — |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- PO4 · Phosphate ion · ion · chains A
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 | 874 | 0.67 | 0.74 | 62 | PO4, MG |
| 2 | 148 | 0.67 | 0.88 | 22 | empty |
| 3 | 263 | 0.65 | 0.83 | 27 | empty |
| 4 | 52 | 0.30 | 0.75 | 11 | empty |
Interfaces
5 interfaces between chains.
- T–P · 526 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–P · 507 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–T · 492 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 383 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 230 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4NLN · Structure of human DNA polymerase beta complexed with nicked DNA containing a template… · 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 4NLN · PDBe 4NLN · UniProt P06746
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