Research workbench
Structure of a small peptide ligand bound to E.COLI DNA sliding clamp
Analyse Structure of a small peptide ligand bound to E.COLI DNA sliding clamp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q4J
- Type
- protein
- Length
- 2,214 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; Peptide ligand
- EC
- 2.7.7.7
- UniProt
- P0A988
- Ligands
- ACE
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 5 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 | 366 | 23% helix, 46% strand | P0A988 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 364 | 22% helix, 44% strand | P0A988 |
| C, D, F | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 365 | 22% helix, 46% strand | P0A988 |
| E | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 364 | 22% helix, 46% strand | P0A988 |
| H, I, J, K, L | Peptide ligand | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 5 copies · chains B, H, C, I, D, J, E, K, F, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.74 | 0.77 | 58 | empty |
| 2 | 749 | 0.72 | 0.78 | 56 | empty |
| 3 | 103 | 0.36 | 0.74 | 23 | empty |
| 4 | 77 | 0.34 | 0.76 | 22 | empty |
| 5 | 67 | 0.33 | 0.76 | 13 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1354 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1338 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1294 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 932 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 713 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
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 3Q4J · PDBe 3Q4J · UniProt P0A988
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