Research workbench
DNA polymerase sliding clamp from Escherichia coli with peptide 4 bound
Analyse DNA polymerase sliding clamp from Escherichia coli with peptide 4 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZG
- Type
- protein
- Length
- 2,984 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.92
- Source
- Escherichia coli 2-427-07_S4_C3; SYNTHETIC CONSTRUCT
- Molecule
- Beta sliding clamp; Peptide 4
- UniProt
- A0A073FMV0
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.92 · 4 distinct chains · 22% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Beta sliding clamp | protein | 367 | 22% helix, 45% strand | A0A073FMV0 |
| B, C, D, E, H | Beta sliding clamp | protein | 368 | 21% helix, 46% strand | A0A073FMV0 |
| G | Beta sliding clamp | protein | 362 | 22% helix, 44% strand | A0A073FMV0 |
| I, J, K, L, M, N, O, P | Peptide 4 | protein | 6 | 0% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.81 | 0.99 | 23 | empty |
| 2 | 1038 | 0.79 | 0.81 | 120 | empty |
| 3 | 1053 | 0.71 | 0.75 | 87 | empty |
| 4 | 566 | 0.70 | 0.79 | 53 | empty |
| 5 | 483 | 0.67 | 0.78 | 46 | empty |
Interfaces
34 interfaces between chains.
- C–D · 1343 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1335 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1296 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1203 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 627 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (nonstandard).
Compared structures
- 7AZG · DNA polymerase sliding clamp from escherichia COLI with peptide 4 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 7AZG · PDBe 7AZG · UniProt A0A073FMV0
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