MolNFT v1 · #61930 · protein + DNA
Insights into the replisome from the crystral structure of the ternary complex of the eubacterial DNA polymerase III alpha-subunit
3E0D · DNA substrate template strand: “Insights into the replisome from the crystral structure of the ternary complex of the eubacterial DNA…”. X-ray diffraction, 2 ligands (DTP, CA), 20 pockets (best druggability 0.82). MolNFT v1 #61930…
- PDB
- 3E0D
- Type
- protein + DNA
- Length
- 2,374 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA substrate template strand; DNA substrate primer strand; DNA polymerase III subunit…
- EC
- 2.7.7.7
- UniProt
- Q9XDH5
- Ligands
- DTP, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA substrate template strand | dna | 20 | — | — |
| D, F | DNA substrate primer strand | dna | 19 | — | — |
| A, B | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1148 | 46% helix, 14% strand | Q9XDH5 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains C, D, A, E, F, B
- 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
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.82 | 0.84 | 106 | empty |
| 2 | 980 | 0.77 | 0.79 | 93 | empty |
| 3 | 791 | 0.76 | 0.80 | 77 | empty |
| 4 | 286 | 0.75 | 0.89 | 34 | empty |
| 5 | 789 | 0.74 | 0.79 | 86 | empty |
Interfaces
7 interfaces between chains.
- E–B · 1035 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–A · 983 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–B · 925 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 916 Ų buried · 119 hydrogen bonds · nucleic-nucleic
- C–D · 904 Ų buried · 108 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified, 1 covalent, 1 isopeptide (nucleotide modification, covalent ligand, isopeptide).
Compared structures
- 3E0D · Insights into the Replisome from the Crystral Structure of the Ternary Complex of the… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9XDH5 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit alpha (Q9XDH5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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
- Elsewhere: RCSB PDB 3E0D · PDBe 3E0D · UniProt Q9XDH5
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