Research workbench
DNA polymerase sliding clamp from escherichia COLI with peptide 8 bound
Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 8 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZF
- Type
- protein
- Length
- 1,490 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Peptide 8
- UniProt
- A0A073FMV0
- Ligands
- SGK, GLN
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta sliding clamp | protein | 369 | 22% helix, 45% strand | A0A073FMV0 |
| C, D | Beta sliding clamp | protein | 368 | 22% helix, 44% strand | A0A073FMV0 |
| H, I, J, K | Peptide 8 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- SGK · 2-(pyridin-2-ylmethylamino)ethanoic acid · ligand · 4 copies · chains A, D, H, B, C, I, J, K
- GLN · Glutamine · ligand · 4 copies · chains A, D, H, B, C, I, J, K
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.73 | 0.78 | 65 | empty |
| 2 | 807 | 0.69 | 0.75 | 61 | SGK, GLN |
| 3 | 746 | 0.68 | 0.75 | 52 | SGK, GLN |
| 4 | 543 | 0.67 | 0.78 | 55 | SGK, GLN |
| 5 | 567 | 0.67 | 0.77 | 52 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1379 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 568 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 538 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 438 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 7AZF · DNA polymerase sliding clamp from Escherichia coli with peptide 8 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 7AZF · PDBe 7AZF · UniProt A0A073FMV0
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