Research workbench
1.98A structure of THIOPHENE1 with S.AUREUS DNA gyrase and DNA
Analyse 1.98A structure of THIOPHENE1 with S.AUREUS DNA gyrase and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NPK
- Type
- protein + DNA
- Length
- 2,767 residues
- Chains
- 8
- 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
- 94H, 9JN, MN, NA, CL, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 48% 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 | 673 | 49% helix, 16% strand | P66937, Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 674 | 48% helix, 17% strand | P66937, Q99XG5 |
| E | 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 | 17 | — | — |
| 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 | 16 | — | — |
| b | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 675 | 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 | 672 | 48% helix, 16% 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 | 20 | — | — |
Ligands and binding sites
- 94H · ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide · ligand · 6 copies · chains B, b, e, f, D, d
- 9JN · ~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide · ligand · 2 copies · chains b, B, e, f
- MN · Manganese (II) ion · metal · 5 copies · chains B, D, b, d
- NA · Sodium ion · metal · chains b
- CL · Chloride ion · ion · chains D
- SO4 · Sulfate ion · ion · chains b, d
- GOL · Glycerol · additive · 13 copies · chains B, D, E, F, b, d, e, f
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.83 | 0.86 | 88 | GOL, MN |
| 2 | 1028 | 0.79 | 0.81 | 61 | 94H, NA, 9JN |
| 3 | 774 | 0.78 | 0.82 | 93 | MN, GOL |
| 4 | 314 | 0.76 | 0.88 | 62 | GOL |
| 5 | 393 | 0.75 | 0.86 | 37 | empty |
Interfaces
15 interfaces between chains.
- b–d · 2512 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2489 Ų buried · 33 hydrogen bonds · protein-protein
- b–e · 1019 Ų buried · 23 hydrogen bonds · protein-nucleic
- d–f · 1006 Ų buried · 27 hydrogen bonds · protein-nucleic
- e–f · 956 Ų buried · 88 hydrogen bonds · nucleic-nucleic
Compared structures
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 5NPK · PDBe 5NPK · UniProt P66937 · UniProt Q99XG5
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