MolNFT v1 · #128421 · protein + DNA
2.22A structure of THIOPHENE2 and GSK945237 with S.AUREUS DNA gyrase and DNA
5NPP · DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase…: “2.22A structure of THIOPHENE2 and GSK945237 with S.AUREUS DNA gyrase and DNA”. X-ray diffraction, 4 ligands (94K, 6EJ, MN), 16 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5NPP
- Type
- protein + DNA
- Length
- 1,382 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- 94K, 6EJ, MN, NA
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 672 | 48% helix, 17% strand | P66937, Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 671 | 49% helix, 17% strand | P66937, Q99XG5 |
| E, F | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 8 | — | — |
| A | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 12 | — | — |
| C | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- 94K · ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide · ligand · 2 copies · chains B, D
- 6EJ · (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one · ligand · chains B, D, A, C
- MN · Manganese (II) ion · metal · 2 copies · chains B, E, D, F
- NA · Sodium ion · metal · chains B
- GOL · Glycerol · additive · 9 copies · chains B, D, F, E, A, C
- DMS · Dimethyl sulfoxide · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.85 | 0.86 | 125 | DMS, GOL, 6EJ |
| 2 | 474 | 0.74 | 0.83 | 35 | empty |
| 3 | 435 | 0.70 | 0.82 | 36 | empty |
| 4 | 514 | 0.65 | 0.77 | 51 | empty |
| 5 | 549 | 0.64 | 0.76 | 53 | empty |
Interfaces
14 interfaces between chains.
- B–D · 3187 Ų buried · 62 hydrogen bonds · protein-protein
- D–A · 789 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–F · 781 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–E · 769 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 731 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5NPP · 2.22A structure of THIOPHENE2 and GSK945237 with S.AUREUS DNA gyrase and DNA · the same entry in another collection · chain C against C, TM-score 1.00
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain B against A, TM-score 0.72
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · 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 P66937
- Every structure of UniProt Q99XG5
- Elsewhere: RCSB PDB 5NPP · PDBe 5NPP · UniProt P66937 · UniProt Q99XG5
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