Research workbench
Structure of poliiialpha-tauc-DNA complex suggests an atomic model of the replisome
Analyse Structure of poliiialpha-tauc-DNA complex suggests an atomic model of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IQJ
- Type
- protein + DNA
- Length
- 5,403 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*CP*GP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*A)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q9XDH5, A0A0M9ACL9
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 13 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G, K | DNA (5'- D(P*CP*GP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*A)-3') | dna | 20 | — | — |
| F | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*GP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP* GP*TP*TP*TP*CP*G)-3') | dna | 20 | — | — |
| H | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*GP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP* GP*TP*TP*TP*CP*G)-3') | dna | 27 | — | — |
| I | DNA (5'- D(P*CP*GP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DOC) )-3') | dna | 21 | — | — |
| J | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*GP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP* GP*TP*TP*TP*CP*G)-3') | dna | 23 | — | — |
| L | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*GP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP* GP*TP*TP*TP*CP*G)-3') | dna | 24 | — | — |
| A | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1164 | 45% helix, 12% strand | Q9XDH5 |
| B | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1167 | 44% helix, 13% strand | Q9XDH5 |
| C | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1166 | 47% helix, 12% strand | Q9XDH5 |
| D | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1185 | 46% helix, 13% strand | Q9XDH5 |
| M | DNA polymerase III subunit GAMMA/TAU (EC 2.7.7.7) | protein | 138 | 31% helix, 0% strand | A0A0M9ACL9 |
| N, O | DNA polymerase III subunit GAMMA/TAU (EC 2.7.7.7) | protein | 135 | 33% helix, 0% strand | A0A0M9ACL9 |
| P | DNA polymerase III subunit GAMMA/TAU (EC 2.7.7.7) | protein | 138 | 29% helix, 0% strand | A0A0M9ACL9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.81 | 0.82 | 108 | empty |
| 2 | 769 | 0.75 | 0.80 | 58 | empty |
| 3 | 977 | 0.71 | 0.76 | 68 | empty |
| 4 | 512 | 0.70 | 0.80 | 43 | empty |
| 5 | 596 | 0.69 | 0.78 | 52 | empty |
Interfaces
25 interfaces between chains.
- G–H · 1030 Ų buried · 107 hydrogen bonds · nucleic-nucleic
- I–J · 1013 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- K–L · 963 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- E–F · 945 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- A–M · 807 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4IQJ · Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome · the same entry in another collection · chain P against P, 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 Q9XDH5
- Every structure of UniProt A0A0M9ACL9
- Elsewhere: RCSB PDB 4IQJ · PDBe 4IQJ · UniProt Q9XDH5 · UniProt A0A0M9ACL9
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