MolNFT v1 · #88097 · protein
Structure of 55 kda N-terminal domain of E. COLI DNA gyrase a subunit with simocyclinone D8 bound
4CKL · DNA gyrase subunit a: “Structure of 55 kda N-terminal domain of E. COLI DNA gyrase a subunit with simocyclinone D8 bound”. X-ray diffraction, 1 ligand (SM8), 10 pockets (best druggability 0.62). MolNFT v1 #88097 on GenesisL1: 3D…
- PDB
- 4CKL
- Type
- protein
- Length
- 884 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- P0AES5
- Ligands
- SM8
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 450 | 48% helix, 14% strand | P0AES5 |
| B | DNA gyrase subunit a (EC 5.99.1.3) | protein | 434 | 46% helix, 15% strand | P0AES5 |
Ligands and binding sites
- SM8 · Simocyclinone D8 · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.62 | 0.80 | 40 | empty |
| 2 | 244 | 0.60 | 0.80 | 34 | empty |
| 3 | 281 | 0.48 | 0.73 | 37 | empty |
| 4 | 129 | 0.44 | 0.77 | 22 | empty |
| 5 | 125 | 0.38 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 360 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4CKL · Structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit with simocycli D8… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AES5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P0AES5) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P0AES5
- Elsewhere: RCSB PDB 4CKL · PDBe 4CKL · UniProt P0AES5
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