Research workbench
Human DNA polymerase beta crosslinked binary complex - a
Analyse Human DNA polymerase beta crosslinked binary complex - a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RBE
- Type
- protein + DNA
- Length
- 346 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, NA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 4 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 | 315 | 52% helix, 13% 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 | 10 | — | — |
| 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
- NA · Sodium ion · metal · 4 copies · chains A, P, D
- CIT · Citric acid · additive · 2 copies · chains A
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 | 1088 | 0.73 | 0.76 | 85 | CIT |
| 2 | 195 | 0.61 | 0.83 | 24 | empty |
Interfaces
5 interfaces between chains.
- P–T · 470 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–T · 456 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 344 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 323 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–T · 228 Ų buried · 20 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 7RBE · PDBe 7RBE · UniProt P06746
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