Research workbench
E.coli sliding clamp in complex with AcALDLF peptide
Analyse E.coli sliding clamp in complex with AcALDLF peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K3M
- Type
- protein
- Length
- 719 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Escherichia coli; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase III subunit beta; Aldlf
- EC
- 2.7.7.7
- UniProt
- P0A988
- Ligands
- CA
- Pockets
- 5 · best druggability 0.43
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 22% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 358 | 22% helix, 43% strand | P0A988 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 358 | 23% helix, 47% strand | P0A988 |
| E | Aldlf | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
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 | 63 | 0.43 | 0.82 | 18 | empty |
| 2 | 65 | 0.31 | 0.75 | 17 | empty |
| 3 | 50 | 0.27 | 0.75 | 16 | empty |
| 4 | 58 | 0.27 | 0.73 | 19 | empty |
| 5 | 55 | 0.27 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1316 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 317 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 4K3M · PDBe 4K3M · UniProt P0A988
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