MolNFT v1 · #59594 · protein + DNA
DNA polymerase beta with a gapped DNA substrate and dumpnpp with manganese in the active site
3C2K: “DNA polymerase beta with a gapped DNA substrate and dumpnpp with manganese in the active site”. X-ray diffraction, 4 ligands (DUP, MN, NA), 3 pockets (best druggability 0.71). MolNFT v1 #59594 on GenesisL1: 3D structure, binding…
- PDB
- 3C2K
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'- D(*DCP*DCP*DGP*DAP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- DUP, MN, NA, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 52% helix, 14% strand | P06746 |
| T | DNA (5'- D(*DCP*DCP*DGP*DAP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP* DGP*DC)-3') | dna | 16 | — | — |
| P | DNA (5'- D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*DGP*DTP*DCP*DGP*DG)-3') | dna | 5 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 5 copies · chains A, P, T
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- CL · Chloride ion · ion · 4 copies · chains 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 | 971 | 0.71 | 0.76 | 68 | DUP, MN |
| 2 | 339 | 0.63 | 0.79 | 29 | empty |
| 3 | 219 | 0.58 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–T · 734 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 466 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–P · 377 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 362 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 226 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Compared structures
- 3C2K · DNA POLYMERASE BETA with a gapped DNA substrate and DUMPNPP with Manganese in the active… · 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 0.95
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 3C2K · PDBe 3C2K · UniProt P06746
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