MolNFT v1 · #73918 · protein + DNA
DNA polymerase beta mutant 5P20 complexed with 6BP of DNA
3OGU: “DNA polymerase beta mutant 5P20 complexed with 6BP of DNA”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.61). MolNFT v1 #73918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OGU
- Type
- protein + DNA
- Length
- 338 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; 5'-D(*CP*AP*TP*CP*TP*G)-3'; 5'-D(P*CP*AP*GP*AP*TP*G)-3'
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- NA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% 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, 13% strand | P06746 |
| T | 5'-D(*CP*AP*TP*CP*TP*G)-3' | dna | 6 | — | — |
| P | 5'-D(P*CP*AP*GP*AP*TP*G)-3' | dna | 6 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, P
- GOL · Glycerol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.61 | 0.82 | 26 | empty |
| 2 | 146 | 0.52 | 0.80 | 20 | empty |
| 3 | 157 | 0.42 | 0.74 | 39 | empty |
| 4 | 57 | 0.27 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–T · 294 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–P · 274 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- A–P · 252 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
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 3OGU · PDBe 3OGU · UniProt P06746
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