MolNFT v1 · #60759 · protein
Crystal structure of E. COLI sliding clamp (beta) bound to a polymerase II peptide
3D1E · DNA polymerase III subunit beta: “Crystal structure of E. COLI sliding clamp (beta) bound to a polymerase II peptide”. X-ray diffraction, 8 pockets (best druggability 0.44). MolNFT v1 #60759 on GenesisL1: 3D structure, binding sites…
- PDB
- 3D1E
- Type
- protein
- Length
- 738 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; Decamer from polymerase II C-terminal
- EC
- 2.7.7.7
- UniProt
- P0A988
- Pockets
- 8 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 366 | 21% helix, 45% strand | P0A988 |
| P | Decamer from polymerase II C-terminal | protein | 6 | 0% helix, 17% strand | — |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.44 | 0.81 | 20 | empty |
| 2 | 162 | 0.42 | 0.74 | 33 | empty |
| 3 | 141 | 0.39 | 0.73 | 26 | empty |
| 4 | 66 | 0.31 | 0.75 | 18 | empty |
| 5 | 76 | 0.31 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1368 Ų buried · 37 hydrogen bonds · protein-protein
- A–P · 524 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3D1E · Crystal structure of E. coli sliding clamp (beta) bound to a polymerase II peptide · the same entry in another collection · chain B against B, TM-score 1.00
- P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A988
- Elsewhere: RCSB PDB 3D1E · PDBe 3D1E · UniProt P0A988
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