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MolNFT v1 · #128416 · protein + DNA

1.98A structure of THIOPHENE1 with S.AUREUS DNA gyrase and DNA

5NPK: “1.98A structure of THIOPHENE1 with S.AUREUS DNA gyrase and DNA”. X-ray diffraction, 6 ligands (94H, 9JN, MN). MolNFT v1 #128416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5NPK
Type
protein + DNA
Length
2,767 residues
Chains
8
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
P66937, Q99XG5
Ligands
94H, 9JN, MN, NA, CL, SO4

Structure

x-ray diffraction · 7 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
B—protein673—P66937, Q99XG5
D—protein674—P66937, Q99XG5
E—dna17——
F—dna16——
b—protein675—P66937, Q99XG5
d—protein672—P66937, Q99XG5
e, f—dna20——

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, E, D, b, d, e

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • 5NPK · 1.98A structure of THIOPHENE1 with S.AUREUS DNA gyrase and DNA · the same entry in another collection · chain f against f, TM-score 1.00
  • Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain d against A, TM-score 0.72

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