Research workbench
Crystal structure of ATP bound desd, the desferrioxamine synthetase from the streptomyces griseoflavus ferrimycin biosynthetic pathway
Analyse Crystal structure of ATP bound desd, the desferrioxamine synthetase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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