Research workbench
Structural plasticity of the bacillus subtilis gyra homodimer
Analyse Structural plasticity of the bacillus subtilis gyra homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DDQ
- Type
- protein
- Length
- 2,733 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- P05653
- Ligands
- K
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 458 | 47% helix, 18% strand | P05653 |
| B | DNA gyrase subunit a (EC 5.99.1.3) | protein | 457 | 49% helix, 15% strand | P05653 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 455 | 47% helix, 16% strand | P05653 |
| D | DNA gyrase subunit a (EC 5.99.1.3) | protein | 455 | 47% helix, 17% strand | P05653 |
| E | DNA gyrase subunit a (EC 5.99.1.3) | protein | 456 | 48% helix, 16% strand | P05653 |
| F | DNA gyrase subunit a (EC 5.99.1.3) | protein | 452 | 47% helix, 15% strand | P05653 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.71 | 0.75 | 104 | empty |
| 2 | 619 | 0.71 | 0.79 | 62 | empty |
| 3 | 520 | 0.67 | 0.78 | 47 | empty |
| 4 | 508 | 0.66 | 0.78 | 47 | empty |
| 5 | 60 | 0.64 | 0.92 | 19 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1174 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1170 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1167 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 754 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 728 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 P05653
- Elsewhere: RCSB PDB 4DDQ · PDBe 4DDQ · UniProt P05653
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