Research workbench
Crystal structure of human primpol ternary complex
Analyse Crystal structure of human primpol ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L2X
- Type
- protein + DNA
- Length
- 556 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed PRIMASE/POLYMERASE protein; DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3'); DNA…
- EC
- 2.7.7.-
- UniProt
- Q96LW4
- Ligands
- DTP, CA
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed PRIMASE/POLYMERASE protein (EC 2.7.7.-) | protein | 271 | 32% helix, 23% strand | Q96LW4 |
| C | DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3') | dna | 12 | — | — |
| D, H | DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3') | dna | 7 | — | — |
| B | DNA-directed PRIMASE/POLYMERASE protein (EC 2.7.7.-) | protein | 251 | 29% helix, 26% strand | Q96LW4 |
| G | DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, C, D, B, G, H
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.70 | 0.78 | 59 | DTP, CA |
| 2 | 469 | 0.64 | 0.77 | 41 | empty |
| 3 | 270 | 0.64 | 0.82 | 33 | DTP, CA |
| 4 | 129 | 0.44 | 0.77 | 22 | empty |
| 5 | 112 | 0.39 | 0.75 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 701 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–G · 374 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 371 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- G–H · 330 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5L2X · Crystal structure of human PrimPol ternary complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q96LW4 · AlphaFold monomer V2.0 prediction for DNA-directed PRIMASE/POLYMERASE protein (Q96LW4) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q96LW4
- Elsewhere: RCSB PDB 5L2X · PDBe 5L2X · UniProt Q96LW4
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