Research workbench
DNA polymerase sliding clamp from escherichia COLI with peptide 36 bound
Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 36 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZ6
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Peptide 36
- UniProt
- A0A073FMV0
- Ligands
- ACE, CL
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 368 | 22% helix, 45% strand | A0A073FMV0 |
| H | Peptide 36 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, H
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.34 | 0.75 | 20 | PEG |
| 2 | 60 | 0.29 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–H · 596 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (nonstandard, covalent ligand).
Compared structures
- 7AZ6 · DNA polymerase sliding clamp from Escherichia coli with peptide 36 bound · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A073FMV0
- Elsewhere: RCSB PDB 7AZ6 · PDBe 7AZ6 · UniProt A0A073FMV0
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