MolNFT v1 · #29798 · protein + DNA
Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus with dgtp
1ZJN · D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3': “Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus with dgtp”. X-ray diffraction, 3 ligands (DGT, NA, MG), 2 pockets (best druggability…
- PDB
- 1ZJN
- Type
- protein + DNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- DGT, NA, MG
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3' | dna | 10 | — | — |
| 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 | 325 | 50% helix, 14% strand | P06746 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains T, P, A
- NA · Sodium ion · metal · 3 copies · chains P, A, D
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.77 | 0.80 | 73 | MG, DGT |
| 2 | 210 | 0.56 | 0.79 | 22 | empty |
Interfaces
5 interfaces between chains.
- T–A · 635 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 444 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- P–A · 392 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 366 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–D · 242 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 1ZJN · Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus… · the same entry in another collection · chain P against P, 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 1ZJN · PDBe 1ZJN · UniProt P06746
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