Research workbench
DNA polymerase sliding clamp from escherichia COLI with peptide 47 bound
Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 47 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZ5
- Type
- protein
- Length
- 1,496 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Peptide 47
- UniProt
- A0A073FMV0
- Ligands
- ACE
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta sliding clamp | protein | 368 | 21% helix, 46% strand | A0A073FMV0 |
| H, I, J, K | Peptide 47 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, D, H, B, C, I, J, K
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.73 | 0.77 | 104 | ACE |
| 2 | 1071 | 0.70 | 0.75 | 85 | ACE |
| 3 | 543 | 0.67 | 0.77 | 54 | empty |
| 4 | 205 | 0.45 | 0.74 | 29 | PG4 |
| 5 | 123 | 0.41 | 0.76 | 20 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1342 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1301 Ų buried · 36 hydrogen bonds · protein-protein
- D–K · 675 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 639 Ų buried · 5 hydrogen bonds · protein-protein
- C–J · 632 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 covalent (nonstandard, covalent ligand).
Compared structures
- 7AZ5 · DNA polymerase sliding clamp from Escherichia coli with peptide 47 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 7AZ5 · PDBe 7AZ5 · UniProt A0A073FMV0
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