MolNFT v1 · #162845 · protein + DNA
E. COLI DNA gyrase - DNA binding and cleavage domain in state 2
6RKV · DNA gyrase subunit a: “E. COLI DNA gyrase - DNA binding and cleavage domain in state 2”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #162845 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RKV
- 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
- 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 | — | — |
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 | 797 | 0.83 | 0.86 | 82 | empty |
| 2 | 673 | 0.82 | 0.86 | 65 | empty |
| 3 | 720 | 0.81 | 0.85 | 65 | empty |
| 4 | 550 | 0.79 | 0.86 | 65 | empty |
| 5 | 171 | 0.76 | 0.92 | 31 | empty |
Interfaces
23 interfaces between chains.
- A–C · 1380 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1283 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1269 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 669 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- F–H · 643 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Compared structures
- 6RKV · E. coli DNA Gyrase - DNA binding and cleavage domain in State 2 · 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 0.95
- 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 0.78
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 6RKV · PDBe 6RKV · UniProt P0AES4 · UniProt P0AES6
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