MolNFT v1 · #101661 · protein + DNA
DNA polymerase beta with O6MG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site
4NY8: “DNA polymerase beta with O6MG in the template base opposite to incoming non-hydrolyzable CTP with manganese…”. X-ray diffraction, 3 ligands (0KX, MN, NA), 2 pockets (best druggability 0.71). MolNFT v1 #101661 on GenesisL1: 3D…
- PDB
- 4NY8
- Type
- protein + DNA
- Length
- 354 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; 5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 0KX, MN, NA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 323 | 50% helix, 13% strand | P06746 |
| T | 5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*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 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P
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 | 1122 | 0.71 | 0.76 | 85 | MN, NA, 0KX |
| 2 | 238 | 0.62 | 0.82 | 26 | empty |
Interfaces
5 interfaces between chains.
- T–P · 486 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–T · 435 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 384 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–P · 337 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 231 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4NY8 · DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable… · 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 4NY8 · PDBe 4NY8 · UniProt P06746
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