MolNFT v1 · #158130 · protein + DNA
Ternary complex crystal structure of K289M variant of DNA polymerase beta with beta-gamma difluoro analogue of dgtp
6NKT: “Ternary complex crystal structure of K289M variant of DNA polymerase beta with beta-gamma difluoro analogue…”. X-ray diffraction, 2 ligands (GFF, NA), 2 pockets (best druggability 0.74). MolNFT v1 #158130 on GenesisL1: 3D structure…
- PDB
- 6NKT
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- GFF, NA
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 321 | 49% helix, 11% strand | P06746 |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- GFF · 2'-deoxy-5'-O-[({[difluoro(phosphono)methyl](hydroxy) phosphoryl}oxy)(hydroxy)phosphoryl]guanosine · ligand · chains A, T, P
- NA · Sodium ion · metal · 2 copies · chains A, P, D
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 | 1037 | 0.74 | 0.77 | 81 | GFF |
| 2 | 256 | 0.62 | 0.81 | 30 | empty |
Interfaces
5 interfaces between chains.
- T–P · 472 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–D · 396 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–T · 393 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–P · 293 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 229 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 6NKT · Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma… · 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 0.92
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 6NKT · PDBe 6NKT · UniProt P06746
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