MolNFT v1 · #97925 · protein
DNA gyrase ATP binding domain of enterococcus faecalis in complex with a small molecule inhibitor ((3S)-1-[2-(PYRIDO[2,3-B]PYRAZIN-7- ylsulfanyl)-9H-PYRIMIDO[4,5-B]INDOL-4-YL]PYRROLIDIN-3-amine)
4KTN · DNA gyrase subunit B: “DNA gyrase ATP binding domain of enterococcus faecalis in complex with a small molecule inhibitor…”. X-ray diffraction, 1 ligand (MJU), 1 pocket (best druggability 0.49). MolNFT v1 #97925 on GenesisL1: 3D…
- PDB
- 4KTN
- Type
- protein
- Length
- 193 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- Q839Z1
- Ligands
- MJU
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 193 | 30% helix, 30% strand | Q839Z1 |
Ligands and binding sites
- MJU · (3S)-1-[2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-9H-pyrimido[4,5-b]indol-4-yl]pyrrolidin-3-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.49 | 0.80 | 23 | MJU |
Compared structures
- 4KTN · Dna gyrase atp binding domain of enterococcus faecalis in complex with a small molecule… · the same entry in another collection · chain A against A, TM-score 1.00
- Q839Z1 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (Q839Z1) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q839Z1
- Elsewhere: RCSB PDB 4KTN · PDBe 4KTN · UniProt Q839Z1
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