MolNFT v1 · #103055 · protein + DNA
Crystal structure of leishmania infantum polymerase beta: nick complex
4P4P · DNA polymerase beta: “Crystal structure of leishmania infantum polymerase beta: nick complex”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.57). MolNFT v1 #103055 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4P4P
- Type
- protein + DNA
- Length
- 301 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3'); DNA (5'-D(P*GP*CP*CP*G)-3')…
- UniProt
- Q9U6N3
- Ligands
- NA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta | protein | 282 | 45% helix, 18% strand | Q9U6N3 |
| C | DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3') | dna | 7 | — | — |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 2 | — | — |
| B | DNA (5'-D(P*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.57 | 0.77 | 33 | empty |
| 2 | 147 | 0.52 | 0.80 | 25 | empty |
| 3 | 173 | 0.43 | 0.74 | 24 | NA |
| 4 | 104 | 0.37 | 0.75 | 21 | empty |
| 5 | 55 | 0.30 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 868 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 514 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–B · 315 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- A–D · 130 Ų buried · 1 hydrogen bond · protein-nucleic
- D–B · 108 Ų buried · 10 hydrogen bonds · nucleic-nucleic
Compared structures
- 4P4P · Crystal structure of Leishmania infantum polymerase beta: Nick 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 4P4P · PDBe 4P4P · UniProt Q9U6N3
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