MolNFT v1 · #119067 · protein + DNA
Cryo-EM structure of the E. COLI replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon, tau complex)
5FKV · DNA polymerase III subunit alpha: “Cryo-EM structure of the E. COLI replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha…”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #119067 on…
- PDB
- 5FKV
- Type
- protein + DNA
- Length
- 2,264 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit alpha; DNA polymerase III beta; DNA polymerase III epsilon…
- EC
- 2.7.7.7
- UniProt
- P10443, P0A988, P03007, P06710
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1145 | 47% helix, 10% strand | P10443 |
| B, C | DNA polymerase III beta (EC 2.7.7.7) | protein | 366 | 22% helix, 46% strand | P0A988 |
| D | DNA polymerase III epsilon (EC 2.7.7.7) | protein | 219 | 38% helix, 16% strand | P03007 |
| E | DNA polymerase III tau (EC 2.7.7.7) | protein | 117 | 61% helix, 7% strand | P06710 |
| P | Primer-template duplex DNA | dna | 25 | — | — |
| T | Primer-template duplex DNA | dna | 26 | — | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.83 | 0.85 | 93 | empty |
| 2 | 1071 | 0.83 | 0.84 | 122 | empty |
| 3 | 107 | 0.79 | 0.97 | 22 | empty |
| 4 | 90 | 0.78 | 0.97 | 20 | empty |
| 5 | 89 | 0.77 | 0.98 | 23 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1920 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1425 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1227 Ų buried · 7 hydrogen bonds · protein-protein
- P–T · 1149 Ų buried · 113 hydrogen bonds · nucleic-nucleic
- B–D · 945 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5FKV · cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA… · the same entry in another collection · chain P against P, 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 0.85
- 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 0.84
- 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 0.77
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 5FKV · PDBe 5FKV · UniProt P10443 · UniProt P0A988 · UniProt P03007 · UniProt P06710
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