Research workbench
Ternary complex of DNA polymerase beta with template fapy-dg and an incoming dctp analog
Analyse Ternary complex of DNA polymerase beta with template fapy-dg and an incoming… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S9P
- 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*(FAP) P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- XC5, MN, NA, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*CP*GP*AP*CP*(FAP) P*TP*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*A)-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, 14% strand | P06746 |
Ligands and binding sites
- XC5 · 2'-deoxy-5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · chains T, P, A
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains D, A, P
- CL · Chloride ion · ion · 2 copies · 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 | 1017 | 0.72 | 0.76 | 70 | XC5, MN |
| 2 | 327 | 0.60 | 0.78 | 27 | empty |
| 3 | 196 | 0.59 | 0.82 | 26 | empty |
Interfaces
5 interfaces between chains.
- T–A · 749 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 478 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- P–A · 394 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 381 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 228 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7S9P · Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog · 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 0.94
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 7S9P · PDBe 7S9P · UniProt P06746
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