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
- 4IRC
- Type
- protein + DNA
- Length
- 751 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q47155
- Ligands
- 0KX, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, B | DNA (5'- D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 18 | — | — |
| H | DNA (5'-D(*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 14 | — | — |
| C | DNA (5'- D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 17 | — | — |
| F, A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 41% helix, 23% strand | Q47155 |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.81 | 0.83 | 76 | 0KX, MG |
| 2 | 1002 | 0.80 | 0.81 | 86 | 0KX, MG |
| 3 | 814 | 0.77 | 0.81 | 59 | empty |
| 4 | 519 | 0.73 | 0.82 | 45 | empty |
| 5 | 65 | 0.38 | 0.79 | 16 | empty |
Interfaces
9 interfaces between chains.
- B–A · 1054 Ų buried · 28 hydrogen bonds · protein-nucleic
- G–F · 963 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 643 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- G–H · 623 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- H–F · 602 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 4IRC · PDBe 4IRC · UniProt Q47155
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