Research workbench
Polymerase-DNA complex
Analyse Polymerase-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IR9
- Type
- protein + DNA
- Length
- 751 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*TP*CP*TP*CP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q47155
- Ligands
- XG4, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, B | DNA (5'- D(P*TP*CP*TP*CP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 18 | — | — |
| C | DNA (5'- D(P*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 17 | — | — |
| H | DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 14 | — | — |
| F, A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 41% helix, 23% strand | Q47155 |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · 2 copies · chains G, H, F, B, C, A
- MG · Magnesium ion · metal · 4 copies · chains F, H, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.80 | 0.83 | 76 | XG4, MG |
| 2 | 1125 | 0.80 | 0.81 | 88 | XG4, MG |
| 3 | 890 | 0.75 | 0.79 | 59 | empty |
| 4 | 730 | 0.73 | 0.79 | 51 | empty |
| 5 | 96 | 0.37 | 0.75 | 14 | empty |
Interfaces
9 interfaces between chains.
- G–F · 957 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–A · 938 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 639 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- G–H · 627 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- C–A · 585 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
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 Q47155
- Elsewhere: RCSB PDB 4IR9 · PDBe 4IR9 · UniProt Q47155
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