Research workbench
DNA polymerase sliding clamp from escherichia COLI with peptide 38 bound
Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 38 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZL
- Type
- protein
- Length
- 1,461 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Peptide 38
- UniProt
- A0A073FMV0
- Ligands
- SJW
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 363 | 22% helix, 47% strand | A0A073FMV0 |
| B | Beta sliding clamp | protein | 358 | 23% helix, 46% strand | A0A073FMV0 |
| C | Beta sliding clamp | protein | 361 | 23% helix, 47% strand | A0A073FMV0 |
| D | Beta sliding clamp | protein | 359 | 23% helix, 47% strand | A0A073FMV0 |
| E, G, F, H | Peptide 38 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- SJW · 3-pyridin-3-ylpropanal · ligand · 4 copies · chains A, B, E, G, C, D, F, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.74 | 0.78 | 77 | empty |
| 2 | 1031 | 0.72 | 0.76 | 70 | SJW |
| 3 | 1002 | 0.71 | 0.75 | 70 | SJW |
| 4 | 562 | 0.68 | 0.78 | 47 | empty |
| 5 | 510 | 0.68 | 0.79 | 43 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1372 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 1296 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 589 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 566 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 560 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 covalent (nonstandard, covalent ligand).
Compared structures
- 7AZL · DNA polymerase sliding clamp from Escherichia coli with peptide 38 bound · the same entry in another collection · chain G against G, 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 7AZL · PDBe 7AZL · UniProt A0A073FMV0
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