MolNFT v1 · #119068 · protein + DNA
Cryo-EM structure of the E. COLI replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon)
5FKW: “Cryo-EM structure of the E. COLI replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha…”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #119068 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5FKW
- Type
- protein + DNA
- Length
- 1,929 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III alpha; DNA polymerase III beta; DNA polymerase III epsilon…
- EC
- 2.7.7.7
- UniProt
- P10443, P0A988, P03007
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III alpha (EC 2.7.7.7) | protein | 927 | 52% helix, 9% 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 | 40% helix, 15% strand | P03007 |
| P | Primer-template duplex DNA | dna | 25 | — | — |
| T | Primer-template duplex DNA | dna | 26 | — | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.80 | 0.83 | 102 | empty |
| 2 | 93 | 0.78 | 0.98 | 23 | empty |
| 3 | 791 | 0.78 | 0.82 | 95 | empty |
| 4 | 66 | 0.75 | 0.98 | 19 | empty |
| 5 | 1147 | 0.75 | 0.78 | 105 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1688 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1438 Ų buried · 30 hydrogen bonds · protein-protein
- P–T · 1165 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- B–D · 961 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 781 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5FKW · cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain C against A, TM-score 0.98
- 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 0.97
- 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
- Elsewhere: RCSB PDB 5FKW · PDBe 5FKW · UniProt P10443 · UniProt P0A988 · UniProt P03007
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