Research workbench
Human DNA polymerase beta crosslinked complex, 20 min ca to mg exchange
Analyse Human DNA polymerase beta crosslinked complex, 20 min ca to mg exchange in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RBN
- Type
- protein + DNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*GP*TP*CP*GP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- QPJ, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 324 | 51% helix, 12% strand | P06746 |
| D | DNA (5'-D(*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 11 | — | — |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
Ligands and binding sites
- QPJ · 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol · ligand · chains A, D
- MG · Magnesium ion · metal · chains A, 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 | 233 | 0.73 | 0.88 | 29 | empty |
| 2 | 1045 | 0.71 | 0.75 | 74 | empty |
| 3 | 199 | 0.59 | 0.82 | 26 | empty |
Interfaces
5 interfaces between chains.
- P–T · 482 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–P · 466 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–T · 416 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 313 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–T · 226 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7RBN · Human DNA polymerase beta crosslinked complex, 20 min Ca to Mg exchange · 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 0.94
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 7RBN · PDBe 7RBN · UniProt P06746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.