Research workbench
DNA polymerase sliding clamp from escherichia COLI with peptide 43 bound
Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 43 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZ8
- Type
- protein
- Length
- 741 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Peptide 43
- UniProt
- A0A073FMV0
- Ligands
- TCA, GLN
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 366 | 22% helix, 45% strand | A0A073FMV0 |
| B | Beta sliding clamp | protein | 365 | 22% helix, 46% strand | A0A073FMV0 |
| H, I | Peptide 43 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- TCA · Phenylethylenecarboxylic acid · ligand · 2 copies · chains A, H, B, I
- GLN · Glutamine · ligand · 2 copies · chains A, H, B, I
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.35 | 0.75 | 16 | empty |
| 2 | 68 | 0.29 | 0.73 | 19 | empty |
| 3 | 63 | 0.29 | 0.74 | 20 | empty |
| 4 | 53 | 0.26 | 0.74 | 18 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1321 Ų buried · 29 hydrogen bonds · protein-protein
- B–I · 477 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 453 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 7AZ8 · DNA polymerase sliding clamp from Escherichia coli with peptide 43 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 7AZ8 · PDBe 7AZ8 · UniProt A0A073FMV0
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