MolNFT v1 · #191555 · protein + DNA
DNA polymerase beta (E.C.2.7.7.7)/DNA complex + 2'- deoxyadenosine-5'-O-(1-thiotriphosphate), soaked in the presence of DATP(ALPHA)S and MNCL2
9ICA · DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'): “DNA polymerase beta (E.C.2.7.7.7)/DNA complex + 2'- deoxyadenosine-5'-O-(1-thiotriphosphate), soaked in the…”. X-ray diffraction, 2 ligands (STP, MN), 5 pockets (best druggability 0.63).…
- PDB
- 9ICA
- Type
- protein + DNA
- Length
- 341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'); DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'); Protein (DNA…
- UniProt
- P06746
- Ligands
- STP, MN
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3') | dna | 7 | — | — |
| P | DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3') | dna | 7 | — | — |
| A | Protein (DNA polymerase beta (E.C.2.7.7.7)) | protein | 327 | 48% helix, 14% strand | P06746 |
Ligands and binding sites
- STP · 2'-deoxyadenosine 5'-O-(1-thiotriphosphate) · ligand · chains P, A
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.63 | 0.83 | 22 | empty |
| 2 | 243 | 0.61 | 0.80 | 22 | empty |
| 3 | 78 | 0.34 | 0.76 | 20 | MN, STP |
| 4 | 68 | 0.31 | 0.75 | 17 | empty |
| 5 | 64 | 0.27 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- P–A · 356 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–P · 324 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- T–A · 299 Ų buried · 6 hydrogen bonds · protein-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 9ICA · PDBe 9ICA · UniProt P06746
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