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Crystal structure of E. COLI sliding clamp (beta) bound to a polymerase III peptide
Analyse Crystal structure of E. COLI sliding clamp (beta) bound to a polymerase III… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D1F
- Type
- protein
- Length
- 750 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; Nonapeptide from polymerase III C-terminal
- EC
- 2.7.7.7
- UniProt
- P0A988
- Ligands
- 323
- Pockets
- 5 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 46% 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, 47% strand | P0A988 |
| P, Q | Nonapeptide from polymerase III C-terminal | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- 323 · 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate · ligand · 2 copies · chains A, P, B, Q
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.36 | 0.73 | 23 | empty |
| 2 | 95 | 0.34 | 0.74 | 27 | empty |
| 3 | 52 | 0.33 | 0.78 | 13 | empty |
| 4 | 88 | 0.32 | 0.73 | 21 | empty |
| 5 | 53 | 0.30 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1324 Ų buried · 36 hydrogen bonds · protein-protein
- B–Q · 716 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 641 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3D1F · Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide · the same entry in another collection · chain A against A, 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
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 3D1F · PDBe 3D1F · UniProt P0A988
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