MolNFT v1 · #103052 · protein + DNA
Crystal structure of leishmania infantum polymerase beta: ternary P/T complex
4P4M · DNA polymerase beta: “Crystal structure of leishmania infantum polymerase beta: ternary P/T complex”. X-ray diffraction, 3 ligands (D3T, MG, NA), 4 pockets (best druggability 0.54). MolNFT v1 #103052 on GenesisL1: 3D structure…
- PDB
- 4P4M
- Type
- protein + DNA
- Length
- 281 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*CP*AP*GP*TP*A)-3'); DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3')
- UniProt
- Q9U6N3
- Ligands
- D3T, MG, NA
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta | protein | 270 | 46% helix, 19% strand | Q9U6N3 |
| D | DNA (5'-D(*CP*AP*GP*TP*A)-3') | dna | 5 | — | — |
| E | DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains A, D, E
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.54 | 0.79 | 25 | D3T, MG |
| 2 | 124 | 0.48 | 0.79 | 22 | empty |
| 3 | 91 | 0.37 | 0.76 | 19 | empty |
| 4 | 57 | 0.25 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–E · 689 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 388 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–E · 257 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Compared structures
- 4P4M · Crystal structure of Leishmania infantum polymerase beta: Ternary P/T complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9U6N3
- Elsewhere: RCSB PDB 4P4M · PDBe 4P4M · UniProt Q9U6N3
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