Research workbench
E. COLI sliding clamp apo-crystal in P21 space group with larger cell dimensions
Analyse E. COLI sliding clamp apo-crystal in P21 space group with larger cell dimensions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PNV
- Type
- protein
- Length
- 732 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta
- EC
- 2.7.7.7
- UniProt
- U6NCW5
- Ligands
- CA, CL
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 366 | 22% helix, 44% strand | U6NCW5 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.55 | 0.78 | 28 | empty |
| 2 | 223 | 0.51 | 0.76 | 28 | PEG, CA |
| 3 | 114 | 0.38 | 0.75 | 22 | CA |
| 4 | 99 | 0.36 | 0.75 | 23 | CA |
| 5 | 79 | 0.32 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1299 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4PNV · E. coli sliding clamp apo-crystal in P21 space group with larger cell dimensions · 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 U6NCW5
- Elsewhere: RCSB PDB 4PNV · PDBe 4PNV · UniProt U6NCW5
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