MolNFT v1 · #111829 · protein + DNA
QUINOLONE(MOXIFLOXACIN)-DNA cleavage complex of gyrase from S. pneumoniae
4Z2C · DNA gyrase subunit a: “QUINOLONE(MOXIFLOXACIN)-DNA cleavage complex of gyrase from S. pneumoniae”. X-ray diffraction, 2 ligands (MFX, MG), 17 pockets (best druggability 0.83). MolNFT v1 #111829 on GenesisL1: 3D structure, binding…
- PDB
- 4Z2C
- Type
- protein + DNA
- Length
- 1,399 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
- MFX, MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 16% 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 | 41% helix, 15% strand | Q59957 |
| B | DNA gyrase subunit a (EC 5.99.1.3) | protein | 482 | 49% helix, 17% strand | Q9R867 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 194 | 40% helix, 13% strand | Q59957 |
| E | Symmetrized E-site DNA | dna | 9 | — | — |
| F | Symmetrized E-site DNA | dna | 13 | — | — |
| H | Symmetrized E-site DNA | dna | 11 | — | — |
| G | Symmetrized E-site DNA | dna | 7 | — | — |
Ligands and binding sites
- MFX · 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid · ligand · 2 copies · chains C, B, F, H, G, A, D, E
- MG · Magnesium ion · metal · 2 copies · chains E, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.83 | 0.84 | 126 | MFX, MG |
| 2 | 484 | 0.74 | 0.83 | 38 | empty |
| 3 | 348 | 0.70 | 0.83 | 44 | empty |
| 4 | 430 | 0.67 | 0.80 | 31 | empty |
| 5 | 404 | 0.67 | 0.80 | 26 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1687 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1393 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 1285 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 685 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 615 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4Z2C · Quinolone(Moxifloxacin)-DNA cleavage complex of gyrase from S. pneumoniae · 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 Q9R867
- Every structure of UniProt Q59957
- Elsewhere: RCSB PDB 4Z2C · PDBe 4Z2C · UniProt Q9R867 · UniProt Q59957
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