Research workbench
DNA polymerase beta I260Q binary complex
Analyse DNA polymerase beta I260Q binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BTE
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA template strand; DNA primer strand; DNA downstream strand
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- NA, IOD, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 324 | 49% helix, 13% strand | P06746 |
| T | DNA template strand | dna | 16 | — | — |
| P | DNA primer strand | dna | 10 | — | — |
| D | DNA downstream strand | dna | 5 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- IOD · Iodide ion · ion · 2 copies · chains A, D
- CL · Chloride ion · ion · chains A
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 | 863 | 0.71 | 0.76 | 67 | empty |
| 2 | 353 | 0.64 | 0.80 | 29 | empty |
| 3 | 206 | 0.57 | 0.80 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–T · 739 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 466 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–P · 402 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 400 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 234 Ų buried · 24 hydrogen bonds · nucleic-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 6BTE · PDBe 6BTE · UniProt P06746
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