Research workbench
Y271G DNA polymerase beta substrate complex with templating cytosine and incoming R8-oxo-GTP
Analyse Y271G DNA polymerase beta substrate complex with templating cytosine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UOK
- Type
- protein + DNA
- Length
- 710 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 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
- 8GT, NA, MN, MG, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, T | DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
| C, P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3') | dna | 10 | — | — |
| E, D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| F | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 50% helix, 14% strand | P06746 |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 322 | 49% helix, 14% strand | P06746 |
Ligands and binding sites
- 8GT · 8-oxo-guanosine-5'-triphosphate · ligand · 2 copies · chains B, C, F, A, T, P
- NA · Sodium ion · metal · 6 copies · chains E, F, C, A, D, P
- MN · Manganese (II) ion · metal · 6 copies · chains F, A
- MG · Magnesium ion · metal · chains T, D
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.76 | 0.78 | 78 | MN, NA, 8GT |
| 2 | 1140 | 0.72 | 0.76 | 81 | 8GT, NA |
| 3 | 329 | 0.61 | 0.79 | 23 | empty |
| 4 | 238 | 0.60 | 0.81 | 27 | empty |
| 5 | 230 | 0.58 | 0.80 | 26 | empty |
Interfaces
12 interfaces between chains.
- B–F · 612 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 473 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- B–C · 466 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–T · 405 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 388 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6UOK · Y271G DNA polymerase beta substrate complex with templating cytosine and incoming… · the same entry in another collection · chain D against D, TM-score 1.00
- P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 6UOK · PDBe 6UOK · UniProt P06746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.