Research workbench
Human DNA polymerase beta ternary complex with templating cytosine and incoming deoxyguanosine diphosphate
Analyse Human DNA polymerase beta ternary complex with templating cytosine and incoming… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K96
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- 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
- DGI, NA, CA, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 51% helix, 13% strand | P06746 |
Ligands and binding sites
- DGI · 2'-deoxyguanosine-5'-diphosphate · ligand · chains T, P, A
- NA · Sodium ion · metal · 4 copies · chains T, P, A, D
- CA · Calcium ion · metal · 3 copies · chains A, P
- CL · Chloride ion · ion · 9 copies · chains T, A, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, T, 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 | 1023 | 0.73 | 0.76 | 58 | CA, DGI |
| 2 | 323 | 0.59 | 0.77 | 32 | CL, EDO |
| 3 | 242 | 0.55 | 0.78 | 25 | empty |
Interfaces
5 interfaces between chains.
- T–A · 659 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 469 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- D–A · 377 Ų buried · 6 hydrogen bonds · protein-nucleic
- P–A · 369 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 243 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 7K96 · Human DNA polymerase beta ternary complex with templating cytosine and incoming… · the same entry in another collection · chain T against T, 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 0.91
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 7K96 · PDBe 7K96 · UniProt P06746
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