MolNFT v1 · #126396 · protein + DNA
Cryo-EM structure of the E. COLI replicative DNA polymerase-clamp- exonuclase-theta complex bound to DNA in the editing mode
5M1S · DNA polymerase III subunit alpha: “Cryo-EM structure of the E. COLI replicative DNA polymerase-clamp- exonuclase-theta complex bound to DNA in…”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #126396 on…
- PDB
- 5M1S
- Type
- protein + DNA
- Length
- 1,983 residues
- Chains
- 7
- 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, P0ABS8
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 927 | 54% helix, 7% strand | P10443 |
| B, C | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 366 | 22% helix, 44% strand | P0A988 |
| D | DNA polymerase III subunit epsilon (EC 2.7.7.7) | protein | 229 | 38% helix, 7% strand | P03007 |
| P | DNA primer strand | dna | 17 | — | — |
| T | DNA template strand | dna | 22 | — | — |
| F | DNA polymerase III subunit theta (EC 2.7.7.7) | protein | 56 | 75% helix, 0% strand | P0ABS8 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.82 | 0.97 | 29 | empty |
| 2 | 153 | 0.82 | 0.97 | 38 | empty |
| 3 | 94 | 0.78 | 0.98 | 29 | empty |
| 4 | 1094 | 0.78 | 0.80 | 98 | empty |
| 5 | 80 | 0.77 | 0.98 | 27 | empty |
Interfaces
14 interfaces between chains.
- A–D · 2155 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1495 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 994 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 786 Ų buried · 14 hydrogen bonds · protein-protein
- A–T · 770 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5M1S · Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta… · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.98
- P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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 0.73
- P0ABS8 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit theta (P0ABS8) · a predicted model of the same protein · chain F against A, TM-score 0.72
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 P0ABS8
- Elsewhere: RCSB PDB 5M1S · PDBe 5M1S · UniProt P10443 · UniProt P0A988 · UniProt P03007 · UniProt P0ABS8
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