Research workbench
3.15A structure of qpt-1 with S.AUREUS DNA gyrase and DNA
Analyse 3.15A structure of qpt-1 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
- 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).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 482 | 50% helix, 18% strand | Q99XG5 |
| B, D, S | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 188 | 46% helix, 13% strand | P66937 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 480 | 50% helix, 18% strand | Q99XG5 |
| E, W | DNA (5'- D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 19 | — | — |
| F, V | DNA (5'- D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 20 | — | — |
| R | DNA gyrase subunit a (EC 5.99.1.3) | protein | 477 | 50% helix, 17% strand | Q99XG5 |
| T | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 48% helix, 16% strand | Q99XG5 |
| U | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 187 | 45% helix, 13% strand | P66937 |
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.84 | 0.85 | 123 | 53L |
| 2 | 1128 | 0.83 | 0.85 | 108 | MN, 50M |
| 3 | 846 | 0.82 | 0.85 | 68 | MN, 53M |
| 4 | 450 | 0.77 | 0.86 | 34 | NA |
| 5 | 262 | 0.73 | 0.87 | 49 | empty |
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
- 5CDO · 3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA · the same entry in another collection · chain W against W, TM-score 1.00
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 Q99XG5
- Every structure of UniProt P66937
- Elsewhere: RCSB PDB 5CDO · PDBe 5CDO · UniProt Q99XG5 · UniProt P66937
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