MolNFT v1 · #158133 · protein + DNA
Ternary complex crystal structure of DNA polymerase beta with "hot- spot sequence" with beta-gamma-methylene dgtp
6NKW · DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)…: “Ternary complex crystal structure of DNA polymerase beta with "hot- spot sequence" with beta-gamma-methylene…”. X-ray diffraction, 4 ligands (GGH, NA, MG), 3 pockets…
- PDB
- 6NKW
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- GGH, NA, MG, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)- 3') (EC 2.7.7.7) | dna | 16 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*TP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 51% helix, 13% strand | P06746 |
Ligands and binding sites
- GGH · 2'-deoxy-5'-O-(hydroxy{[hydroxy(phosphonomethyl) phosphoryl]oxy}phosphoryl)guanosine · ligand · chains T, P, A
- NA · Sodium ion · metal · 3 copies · chains P, A, D
- MG · Magnesium ion · metal · 2 copies · chains T, A
- 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 | 958 | 0.72 | 0.76 | 68 | MG, GGH |
| 2 | 325 | 0.63 | 0.80 | 30 | MG |
| 3 | 209 | 0.55 | 0.79 | 26 | empty |
Interfaces
5 interfaces between chains.
- T–A · 728 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 447 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- P–A · 393 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 385 Ų buried · 8 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
- 6NKW · Ternary complex crystal structure of DNA polymerase Beta with hot-spot sequence" with… · 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 6NKW · PDBe 6NKW · UniProt P06746
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