Research workbench
Crystal structure of N-terminal domain of gyra with the antibiotic simocyclinone D8
Analyse Crystal structure of N-terminal domain of gyra with the antibiotic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y3P
- Type
- protein
- Length
- 1,002 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- P0AES5
- Ligands
- SM8, MG
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 496 | 45% helix, 16% strand | P0AES5 |
| B | DNA gyrase subunit a (EC 5.99.1.3) | protein | 506 | 46% helix, 17% strand | P0AES5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.67 | 0.77 | 68 | empty |
| 2 | 310 | 0.63 | 0.80 | 44 | empty |
| 3 | 71 | 0.54 | 0.86 | 22 | empty |
| 4 | 253 | 0.50 | 0.74 | 43 | empty |
| 5 | 112 | 0.48 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1783 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2Y3P · Crystal structure of N-terminal domain of GyrA with the antibiotic simocycli D8 · the same entry in another collection · chain A against A, TM-score 1.00
- P0AES5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P0AES5) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0AES5
- Elsewhere: RCSB PDB 2Y3P · PDBe 2Y3P · UniProt P0AES5
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