Research workbench
A domain insertion in E. COLI gyrb adopts a novel fold that plays a critical role in gyrase function
Analyse A domain insertion in E. COLI gyrb adopts a novel fold that plays a critical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NUH
- Type
- protein
- Length
- 839 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- P0AES4, P0AES6
- Ligands
- MG
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 485 | 47% helix, 15% strand | P0AES4 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 354 | 46% helix, 22% strand | P0AES6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.61 | 0.75 | 57 | empty |
| 2 | 153 | 0.60 | 0.83 | 27 | empty |
| 3 | 292 | 0.58 | 0.77 | 35 | empty |
| 4 | 75 | 0.51 | 0.84 | 16 | empty |
| 5 | 245 | 0.51 | 0.75 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 760 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 3NUH · A domain insertion in E. coli GyrB adopts a novel fold that plays a critical role in… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AES4 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P0AES4) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · a predicted model of the same protein · chain B against A, TM-score 0.79
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 P0AES4
- Every structure of UniProt P0AES6
- Elsewhere: RCSB PDB 3NUH · PDBe 3NUH · UniProt P0AES4 · UniProt P0AES6
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