MolNFT v1 · #68756 · protein + DNA
Crystal structure of E.COLI pol II-abasic DNA-datp LT(0, 3) ternary complex
3K5L · DNA polymerase II: “Crystal structure of E.COLI pol II-abasic DNA-datp LT(0, 3) ternary complex”. X-ray diffraction, 2 ligands (DTP, MG), 6 pockets (best druggability 0.81). MolNFT v1 #68756 on GenesisL1: 3D structure, binding sites…
- PDB
- 3K5L
- Type
- protein + DNA
- Length
- 812 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase II; DNA (5'-D(*TP*AP*TP*(3DR) P*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3…
- EC
- 2.7.7.7
- UniProt
- P21189
- Ligands
- DTP, MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase II (EC 2.7.7.7) | protein | 781 | 39% helix, 25% strand | P21189 |
| T | DNA (5'-D(*TP*AP*TP*(3DR) P*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3') | dna | 18 | — | — |
| P | DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*(DOC))-3') | dna | 13 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.81 | 0.82 | 125 | empty |
| 2 | 87 | 0.73 | 0.96 | 25 | empty |
| 3 | 226 | 0.66 | 0.84 | 32 | DTP, MG |
| 4 | 220 | 0.52 | 0.76 | 29 | empty |
| 5 | 105 | 0.49 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1438 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 799 Ų buried · 21 hydrogen bonds · protein-nucleic
- T–P · 616 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3K5L · Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- P21189 · AlphaFold monomer V2.0 prediction for DNA polymerase II (P21189) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P21189
- Elsewhere: RCSB PDB 3K5L · PDBe 3K5L · UniProt P21189
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