MolNFT v1 · #119066 · protein
Cryo-EM structure of the E. COLI replicative DNA polymerase complex in DNA free state (DNA polymerase III alpha, beta, epsilon, tau complex)
5FKU · DNA polymerase III subunit alpha: “Cryo-EM structure of the E. COLI replicative DNA polymerase complex in DNA free state (DNA polymerase III…”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #119066 on…
- PDB
- 5FKU
- Type
- protein
- Length
- 2,219 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit alpha; DNA polymerase III subunit beta; DNA polymerase III…
- EC
- 2.7.7.7
- UniProt
- P10443, P0A988, P03007, P06710
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1149 | 46% helix, 10% strand | P10443 |
| B, C | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 366 | 22% helix, 43% strand | P0A988 |
| D | DNA polymerase III subunit epsilon (EC 2.7.7.7) | protein | 218 | 40% helix, 12% strand | P03007 |
| E | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 120 | 58% helix, 14% strand | P06710 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.80 | 0.85 | 77 | empty |
| 2 | 85 | 0.78 | 0.98 | 23 | empty |
| 3 | 122 | 0.73 | 0.93 | 36 | empty |
| 4 | 579 | 0.71 | 0.79 | 70 | empty |
| 5 | 50 | 0.70 | 0.98 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1808 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1457 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 801 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 768 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 607 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5FKU · cryo-EM structure of the E. coli replicative DNA polymerase complex in DNA free state… · the same entry in another collection · chain E against E, TM-score 1.00
- P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P06710 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit tau (P06710) · a predicted model of the same protein · chain E against A, TM-score 0.93
- P10443 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit alpha (P10443) · a predicted model of the same protein · chain A against A, TM-score 0.85
- P03007 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit epsilon (P03007) · a predicted model of the same protein · chain D against A, TM-score 0.78
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 P10443
- Every structure of UniProt P0A988
- Every structure of UniProt P03007
- Every structure of UniProt P06710
- Elsewhere: RCSB PDB 5FKU · PDBe 5FKU · UniProt P10443 · UniProt P0A988 · UniProt P03007 · UniProt P06710
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