Research workbench
Dihedral oligomeric complex of gyra N-terminal fragment with DNA, solved by cryoem in C2 symmetry
Analyse Dihedral oligomeric complex of gyra N-terminal fragment with DNA, solved by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N1P
- Type
- protein + DNA
- Length
- 3,916 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA (44-mer)
- EC
- 5.99.1.3
- UniProt
- A0A0Y2BJX7
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | DNA gyrase subunit a (EC 5.99.1.3) | protein | 476 | 47% helix, 11% strand | A0A0Y2BJX7 |
| B, D, F, H | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 47% helix, 11% strand | A0A0Y2BJX7 |
| I | DNA (44-mer) | dna | 44 | — | — |
| J | DNA (44-mer) | dna | 44 | — | — |
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 | 804 | 0.85 | 0.88 | 137 | empty |
| 2 | 783 | 0.85 | 0.88 | 129 | empty |
| 3 | 546 | 0.84 | 0.90 | 101 | empty |
| 4 | 781 | 0.84 | 0.87 | 118 | empty |
| 5 | 908 | 0.84 | 0.85 | 143 | empty |
Interfaces
31 interfaces between chains.
- I–J · 2095 Ų buried · 236 hydrogen bonds · nucleic-nucleic
- E–F · 1080 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1077 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1076 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6N1P · Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0Y2BJX7
- Elsewhere: RCSB PDB 6N1P · PDBe 6N1P · UniProt A0A0Y2BJX7
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