Research workbench
E. COLI DNA gyrase - DNA binding and cleavage domain in state 1
Analyse E. COLI DNA gyrase - DNA binding and cleavage domain in state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RKU
- Type
- protein + DNA
- Length
- 1,848 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA gyrase subunit B; DNA strand 1; DNA strand 2
- EC
- 5.6.2.3
- UniProt
- P0AES4, P0AES6
- Ligands
- JHN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA gyrase subunit a (EC 5.6.2.3) | protein | 511 | 45% helix, 14% strand | P0AES4 |
| B, D | DNA gyrase subunit B (EC 5.6.2.3) | protein | 381 | 40% helix, 16% strand | P0AES6 |
| F, E | DNA strand 1 | dna | 14 | — | — |
| G, H | DNA strand 2 | dna | 18 | — | — |
Ligands and binding sites
- JHN · (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione · ligand · chains A, C, G, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.83 | 0.87 | 77 | empty |
| 2 | 1104 | 0.81 | 0.82 | 120 | empty |
| 3 | 1100 | 0.81 | 0.82 | 127 | empty |
| 4 | 664 | 0.79 | 0.84 | 51 | empty |
| 5 | 185 | 0.77 | 0.92 | 31 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1496 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1450 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1412 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 730 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6RKU · E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 · the same entry in another collection · chain H against H, TM-score 1.00
- P0AES4 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P0AES4) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · a predicted model of the same protein · chain D against A, TM-score 0.78
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 6RKU · PDBe 6RKU · UniProt P0AES4 · UniProt P0AES6
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