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MolNFT v1 · #115239 · protein + DNA

3.15A structure of qpt-1 with S.AUREUS DNA gyrase and DNA

5CDO · DNA gyrase subunit a: “3.15A structure of qpt-1 with S.AUREUS DNA gyrase and DNA”. X-ray diffraction, 6 ligands (53M, 53L, 50M), 20 pockets (best druggability 0.84). MolNFT v1 #115239 on GenesisL1: 3D structure, binding sites and…

PDB
5CDO
Type
protein + DNA
Length
2,749 residues
Chains
12
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA gyrase subunit a; DNA gyrase subunit B,DNA gyrase subunit B; DNA (5'…
EC
5.99.1.3
UniProt
Q99XG5, P66937
Ligands
53M, 53L, 50M, NA, MN, SO4
Pockets
20 · best druggability 0.84

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA gyrase subunit a (EC 5.99.1.3)protein48250% helix, 18% strandQ99XG5
B, D, SDNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3)protein18846% helix, 13% strandP66937
CDNA gyrase subunit a (EC 5.99.1.3)protein48050% helix, 18% strandQ99XG5
E, WDNA (5'- D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')dna19——
F, VDNA (5'- D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')dna20——
RDNA gyrase subunit a (EC 5.99.1.3)protein47750% helix, 17% strandQ99XG5
TDNA gyrase subunit a (EC 5.99.1.3)protein48148% helix, 16% strandQ99XG5
UDNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3)protein18745% helix, 13% strandP66937

Ligands and binding sites

  • 53M · (2r,4s,4as)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4, 4A-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one · ligand · 2 copies · chains A, B, C, E, F, R, T, U, V, W
  • 53L · (2r,4s,4as,5s)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4, 4A-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione · ligand · chains A, C, D, E, F
  • 50M · (2r,4s,4as,5r)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4, 4A-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione · ligand · chains R, S, T, V, W
  • NA · Sodium ion · metal · 5 copies · chains A, C, R, T
  • MN · Manganese (II) ion · metal · 4 copies · chains B, D, S, U
  • SO4 · Sulfate ion · ion · 3 copies · chains A, C, R, T
  • GOL · Glycerol · additive · 5 copies · chains A, D, E, U, W

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110660.840.8512353L
211280.830.85108MN, 50M
38460.820.8568MN, 53M
44500.770.8634NA
52620.730.8749empty

Interfaces

30 interfaces between chains.

  • A–C · 1792 Ų buried · 29 hydrogen bonds · protein-protein
  • R–T · 1618 Ų buried · 26 hydrogen bonds · protein-protein
  • A–B · 1386 Ų buried · 14 hydrogen bonds · protein-protein
  • R–S · 1381 Ų buried · 14 hydrogen bonds · protein-protein
  • C–D · 1314 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

  • Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain A against A, TM-score 0.99
  • 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 0.98

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