Research workbench
DNA polymerase sliding clamp from escherichia COLI with peptide 18 bound
Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 18 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZE
- Type
- protein
- Length
- 740 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Peptide 18
- UniProt
- A0A073FMV0
- Ligands
- SJ8, GLN
- Pockets
- 5 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 368 | 21% helix, 46% strand | A0A073FMV0 |
| B | Beta sliding clamp | protein | 364 | 21% helix, 45% strand | A0A073FMV0 |
| H, I | Peptide 18 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- SJ8 · (~{E})-3-(4-fluorophenyl)prop-2-enoic acid · ligand · 2 copies · chains A, H, B, I
- GLN · Glutamine · ligand · 2 copies · chains A, H, B, I
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, B, I
- GOL · Glycerol · additive · 2 copies · chains A, B
- MLI · Malonate ion · additive · chains A
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 | 82 | 0.35 | 0.75 | 14 | empty |
| 2 | 70 | 0.31 | 0.74 | 18 | empty |
| 3 | 56 | 0.28 | 0.74 | 21 | empty |
| 4 | 50 | 0.28 | 0.75 | 18 | empty |
| 5 | 59 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1305 Ų buried · 30 hydrogen bonds · protein-protein
- B–I · 443 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 421 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 7AZE · DNA polymerase sliding clamp from Escherichia coli with peptide 18 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 7AZE · PDBe 7AZE · UniProt A0A073FMV0
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