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Ternary complex crystal structure of DNA polymerase beta with 5- hydroxymethyl-dc (5-hmc) at the templating position
Analyse Ternary complex crystal structure of DNA polymerase beta with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N2T
- 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(*CP*CP*GP*AP*CP*(5HC) P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 1GC, MG, NA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 53% 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 | 53% helix, 14% strand | P06746 |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*(5HC) P*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*C)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- 1GC · 2'-deoxy-5'-O-[(R)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]guanosine · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, 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
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 | 686 | 0.70 | 0.78 | 57 | MG, 1GC |
| 2 | 238 | 0.61 | 0.81 | 28 | empty |
| 3 | 203 | 0.59 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–T · 731 Ų buried · 19 hydrogen bonds · protein-nucleic
- T–P · 464 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–P · 383 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 360 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 239 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6N2T · Ternary complex crystal structure of DNA polymerase Beta with 5-hydroxymethyl-dC (5-hmC)… · 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 6N2T · PDBe 6N2T · UniProt P06746
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