Research workbench
Crystal structure of leishmania infantum polymerase beta: ternary gap complex
Analyse Crystal structure of leishmania infantum polymerase beta: ternary gap complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P4O
- Type
- protein + DNA
- Length
- 325 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*T)-3'); DNA (5'-D(P*GP*CP*CP*G)-3'); DNA…
- UniProt
- Q9U6N3
- Ligands
- D3T, NA, MG
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta | protein | 306 | 46% helix, 17% strand | Q9U6N3 |
| E | DNA (5'-D(*CP*AP*GP*TP*AP*T)-3') | dna | 6 | — | — |
| G | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 3 | — | — |
| F | DNA (5'-D(P*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains A, E, F
- NA · Sodium ion · metal · 2 copies · chains A, E, F
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.61 | 0.78 | 38 | D3T, MG |
| 2 | 159 | 0.50 | 0.79 | 19 | empty |
| 3 | 233 | 0.44 | 0.73 | 29 | NA |
| 4 | 160 | 0.41 | 0.74 | 24 | empty |
| 5 | 63 | 0.34 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–F · 826 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–E · 374 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 284 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- A–G · 268 Ų buried · 4 hydrogen bonds · protein-nucleic
- G–F · 139 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 4P4O · Crystal structure of Leishmania infantum polymerase beta: Ternary gap 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 4P4O · PDBe 4P4O · UniProt Q9U6N3
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