Research workbench
Apo structure of 55 kda N-terminal domain of E. COLI DNA gyrase a subunit
Analyse Apo structure of 55 kda N-terminal domain of E. COLI DNA gyrase a subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CKK
- Type
- protein
- Length
- 1,937 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- P0AES5
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 17% 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 | P0AES5 |
| B, D | DNA gyrase subunit a (EC 5.99.1.3) | protein | 484 | 46% helix, 17% strand | P0AES5 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 484 | 46% helix, 18% strand | P0AES5 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.69 | 0.74 | 85 | empty |
| 2 | 543 | 0.63 | 0.75 | 54 | empty |
| 3 | 131 | 0.62 | 0.86 | 23 | empty |
| 4 | 95 | 0.59 | 0.87 | 21 | empty |
| 5 | 270 | 0.58 | 0.79 | 38 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1819 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1811 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- P0AES5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P0AES5) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 4CKK · PDBe 4CKK · UniProt P0AES5
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