MolNFT v1 · #188195 · protein
Crystal structure of ATP bound desd, the desferrioxamine synthetase from the streptomyces griseoflavus ferrimycin biosynthetic pathway
7TGK · Desferrioxamine synthetase desd: “Crystal structure of ATP bound desd, the desferrioxamine synthetase from the streptomyces griseoflavus…”. X-ray diffraction, 3 ligands (ATP, MG, SO4), 20 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 7TGK
- Type
- protein
- Length
- 2,963 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desferrioxamine synthetase desd
- Ligands
- ATP, MG, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, E | Desferrioxamine synthetase desd | protein | 593 | 44% helix, 21% strand | — |
| A, C | Desferrioxamine synthetase desd | protein | 592 | 43% helix, 21% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains D, B, E, A, C
- MG · Magnesium ion · metal · 10 copies · chains D, B, E, A, C
- SO4 · Sulfate ion · ion · 39 copies · chains D, C, B, A, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains D, B, E, A, C
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.88 | 0.89 | 119 | SO4, ATP |
| 2 | 1121 | 0.87 | 0.88 | 112 | SO4, ATP, MG, MPD |
| 3 | 1185 | 0.86 | 0.87 | 122 | SO4, ATP, MG |
| 4 | 596 | 0.86 | 0.91 | 80 | SO4, ATP, MG |
| 5 | 1165 | 0.84 | 0.85 | 99 | SO4, ATP |
Interfaces
6 interfaces between chains.
- B–A · 2216 Ų buried · 12 hydrogen bonds · protein-protein
- D–C · 2179 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 562 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 508 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 488 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7TGK · Crystal structure of ATP bound DesD, the desferrioxamine synthetase from the Streptomyces… · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 7TGK · PDBe 7TGK
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