MolNFT v1 · #171330 · protein + DNA
Ternary complex of staphylococcus aureus DNA gyrase with AMK12 and DNA
6Z1A · DNA gyrase subunit B,DNA gyrase subunit a: “Ternary complex of staphylococcus aureus DNA gyrase with AMK12 and DNA”. X-ray diffraction, 3 ligands (Q52, MN, CL), 15 pockets (best druggability 0.85). MolNFT v1 #171330 on GenesisL1: 3D…
- PDB
- 6Z1A
- Type
- protein + DNA
- Length
- 1,381 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit a; DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3'); DNA…
- EC
- 5.6.2.2
- UniProt
- P0A0K8, P20831
- Ligands
- Q52, MN, CL
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B,DNA gyrase subunit a (EC 5.6.2.2) | protein | 671 | 48% helix, 17% strand | P0A0K8, P20831 |
| D | DNA gyrase subunit B,DNA gyrase subunit a (EC 5.6.2.2) | protein | 671 | 49% helix, 16% strand | P0A0K8, P20831 |
| E, F | DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3') | dna | 8 | — | — |
| G | DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 12 | — | — |
| H | DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- Q52 · ~{N}-[(4-chlorophenyl)methyl]-1-[2-(6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-amine · ligand · chains B, D, G, H
- MN · Manganese (II) ion · metal · 4 copies · chains B, D, F, H, E, G
- CL · Chloride ion · ion · chains B, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains D, F, B, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, E, H, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.85 | 0.86 | 129 | DMS, Q52, MN |
| 2 | 442 | 0.74 | 0.84 | 34 | EPE |
| 3 | 400 | 0.69 | 0.81 | 32 | EPE |
| 4 | 483 | 0.65 | 0.78 | 77 | empty |
| 5 | 533 | 0.64 | 0.76 | 54 | empty |
Interfaces
14 interfaces between chains.
- B–D · 2932 Ų buried · 37 hydrogen bonds · protein-protein
- D–G · 857 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–F · 787 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–E · 785 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–H · 760 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6Z1A · Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA · the same entry in another collection · chain H against H, 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 B 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 6Z1A · PDBe 6Z1A · UniProt P0A0K8 · UniProt P20831
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