MolNFT v1 · #111831 · protein + DNA
QUINOLONE(TROVAFLOXACIN)-DNA cleavage complex of gyrase from S. pneumoniae
4Z2E · DNA gyrase subunit a: “QUINOLONE(TROVAFLOXACIN)-DNA cleavage complex of gyrase from S. pneumoniae”. X-ray diffraction, 2 ligands (TR6, MG), 20 pockets (best druggability 0.82). MolNFT v1 #111831 on GenesisL1: 3D structure, binding…
- PDB
- 4Z2E
- Type
- protein + DNA
- Length
- 1,383 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
- TR6, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 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 | 47% helix, 18% strand | Q9R867 |
| C | DNA gyrase subunit B (EC 5.99.1.3) | protein | 197 | 39% helix, 13% strand | Q59957 |
| B | DNA gyrase subunit a (EC 5.99.1.3) | protein | 472 | 50% helix, 15% strand | Q9R867 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 191 | 41% helix, 13% strand | Q59957 |
| E | Symmetrized E-site DNA | dna | 8 | — | — |
| F | Symmetrized E-site DNA | dna | 12 | — | — |
| H | Symmetrized E-site DNA | dna | 11 | — | — |
| G | Symmetrized E-site DNA | dna | 7 | — | — |
Ligands and binding sites
- TR6 · Trovafloxacin · ligand · 2 copies · chains C, B, F, H, G, A, D, E
- MG · Magnesium ion · metal · 2 copies · chains B, F, G, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.82 | 0.89 | 67 | empty |
| 2 | 414 | 0.78 | 0.87 | 66 | empty |
| 3 | 455 | 0.78 | 0.86 | 68 | TR6, MG |
| 4 | 176 | 0.75 | 0.91 | 37 | empty |
| 5 | 374 | 0.68 | 0.81 | 43 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1260 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 1185 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1080 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 506 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–C · 412 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4Z2E · Quinolone(Trovafloxacin)-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 4Z2E · PDBe 4Z2E · UniProt Q9R867 · UniProt Q59957
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