Research workbench
E. COLI sliding clamp in complex with 6-nitroindazole
Analyse E. COLI sliding clamp in complex with 6-nitroindazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N96
- Type
- protein
- Length
- 717 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
- P0A988
- Ligands
- 6NI, CA, CL
- Pockets
- 7 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 356 | 22% helix, 47% strand | P0A988 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 361 | 23% helix, 44% strand | P0A988 |
Ligands and binding sites
- 6NI · 6-nitroindazole · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.38 | 0.75 | 23 | empty |
| 2 | 87 | 0.34 | 0.75 | 21 | CA |
| 3 | 64 | 0.33 | 0.76 | 12 | empty |
| 4 | 60 | 0.31 | 0.76 | 15 | CL |
| 5 | 68 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1339 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 P0A988
- Elsewhere: RCSB PDB 4N96 · PDBe 4N96 · UniProt P0A988
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.