MolNFT v1 · #111830 · protein + DNA
QUINOLONE(LEVOFLOXACIN)-DNA cleavage complex of gyrase from S. pneumoniae
4Z2D · DNA gyrase subunit a: “QUINOLONE(LEVOFLOXACIN)-DNA cleavage complex of gyrase from S. pneumoniae”. X-ray diffraction, 2 ligands (LFX, MG), 20 pockets (best druggability 0.81). MolNFT v1 #111830 on GenesisL1: 3D structure, binding…
- PDB
- 4Z2D
- Type
- protein + DNA
- Length
- 1,384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA gyrase subunit B; Symmetrized E-site DNA
- EC
- 5.99.1.3
- UniProt
- Q9R867, Q59957
- Ligands
- LFX, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 485 | 48% helix, 18% strand | Q9R867 |
| C | DNA gyrase subunit B (EC 5.99.1.3) | protein | 198 | 38% helix, 15% strand | Q59957 |
| B | DNA gyrase subunit a (EC 5.99.1.3) | protein | 471 | 50% helix, 15% strand | Q9R867 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 194 | 43% helix, 11% strand | Q59957 |
| E, G | Symmetrized E-site DNA | dna | 7 | — | — |
| F, H | Symmetrized E-site DNA | dna | 11 | — | — |
Ligands and binding sites
- LFX · (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid · ligand · 2 copies · chains C, B, F, H, G, A, D, E
- MG · Magnesium ion · metal · 2 copies · chains E, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.81 | 0.89 | 73 | empty |
| 2 | 165 | 0.74 | 0.91 | 37 | empty |
| 3 | 386 | 0.74 | 0.85 | 63 | empty |
| 4 | 316 | 0.74 | 0.86 | 49 | LFX |
| 5 | 53 | 0.69 | 0.98 | 18 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1386 Ų buried · 14 hydrogen bonds · protein-protein
- C–B · 1283 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1104 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 595 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4Z2D · Quinolone(Levofloxacin)-DNA cleavage complex of gyrase from S. pneumoniae · the same entry in another collection · chain C against C, 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 Q9R867
- Every structure of UniProt Q59957
- Elsewhere: RCSB PDB 4Z2D · PDBe 4Z2D · UniProt Q9R867 · UniProt Q59957
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