MolNFT v1 · #162842 · protein + DNA
E. COLI DNA gyrase - DNA binding and cleavage domain in state 1 without toprim insertion
6RKS · DNA gyrase subunit a: “E. COLI DNA gyrase - DNA binding and cleavage domain in state 1 without toprim insertion”. Electron microscopy, 1 ligand (JHN), 20 pockets (best druggability 0.83). MolNFT v1 #162842 on GenesisL1: 3D…
- PDB
- 6RKS
- Type
- protein + DNA
- Length
- 1,480 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
- 5.6.2.2
- UniProt
- P0AES4, P0AES6
- Ligands
- JHN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA gyrase subunit a (EC 5.6.2.2) | protein | 508 | 44% helix, 13% strand | P0AES4 |
| B, D | DNA gyrase subunit B (EC 5.6.2.2) | protein | 200 | 31% helix, 14% 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 | 743 | 0.83 | 0.87 | 70 | empty |
| 2 | 699 | 0.78 | 0.83 | 47 | empty |
| 3 | 764 | 0.76 | 0.81 | 85 | empty |
| 4 | 124 | 0.75 | 0.93 | 27 | empty |
| 5 | 763 | 0.74 | 0.80 | 81 | empty |
Interfaces
23 interfaces between chains.
- A–C · 1424 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1172 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1155 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 699 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 691 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6RKS · E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.91
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 6RKS · PDBe 6RKS · UniProt P0AES4 · UniProt P0AES6
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