MolNFT v1 · #103592 · protein + DNA
Crystal structure of S.A. gyrase-AM8191 complex
4PLB · DNA (5'- D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP…: “Crystal structure of S.A. gyrase-AM8191 complex”. X-ray diffraction, 3 ligands (31N, MN, SO4), 16 pockets (best druggability 0.80). MolNFT v1 #103592 on GenesisL1: 3D…
- PDB
- 4PLB
- Type
- protein + DNA
- Length
- 1,381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3'); Chimera…
- EC
- 5.99.1.3
- UniProt
- P0A0K8, P20831
- Ligands
- 31N, MN, SO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 20 | — | — |
| F | DNA (5'- D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 19 | — | — |
| B | Chimera protein of DNA gyrase subunits B and a (EC 5.99.1.3) | protein | 672 | 49% helix, 16% strand | P0A0K8, P20831 |
| D | Chimera protein of DNA gyrase subunits B and a (EC 5.99.1.3) | protein | 670 | 49% helix, 16% strand | P0A0K8, P20831 |
Ligands and binding sites
- 31N · 6-[({(1r,4S)-1-[(1S)-2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)-1-hydroxyethyl]-2-oxabicyclo[2.2.2]oct-4-yl}amino)methyl]-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one · ligand · chains E, F, B, D
- MN · Manganese (II) ion · metal · 2 copies · chains E, B, F, D
- SO4 · Sulfate ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.80 | 0.85 | 72 | 31N |
| 2 | 262 | 0.76 | 0.89 | 37 | empty |
| 3 | 482 | 0.74 | 0.83 | 35 | empty |
| 4 | 407 | 0.67 | 0.80 | 29 | empty |
| 5 | 539 | 0.65 | 0.77 | 53 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3090 Ų buried · 48 hydrogen bonds · protein-protein
- E–B · 998 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–D · 992 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–F · 928 Ų buried · 108 hydrogen bonds · nucleic-nucleic
- E–D · 847 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 4PLB · Crystal Structure of S.A. gyrase-AM8191 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P20831 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P20831) · a predicted model of the same protein · chain B against A, TM-score 0.72
- P0A0K8 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0A0K8) · a predicted model of the same protein · chain D against A, TM-score 0.28
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 P0A0K8
- Every structure of UniProt P20831
- Elsewhere: RCSB PDB 4PLB · PDBe 4PLB · UniProt P0A0K8 · UniProt P20831
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