Research workbench
Crystal structure of AMP+PPI bound desd, the desferrioxamine synthetase from the streptomyces griseoflavus ferrimycin biosynthetic pathway
Analyse Crystal structure of AMP+PPI bound desd, the desferrioxamine synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TGL
- Type
- protein
- Length
- 2,955 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desferrioxamine synthetase desd
- Ligands
- PPV, AMP, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desferrioxamine synthetase desd | protein | 590 | 42% helix, 20% strand | — |
| B | Desferrioxamine synthetase desd | protein | 592 | 41% helix, 20% strand | — |
| C, E | Desferrioxamine synthetase desd | protein | 591 | 42% helix, 20% strand | — |
| D | Desferrioxamine synthetase desd | protein | 591 | 42% helix, 21% strand | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 5 copies · chains A, B, C, D, E
- AMP · Adenosine monophosphate · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, E
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.86 | 0.87 | 116 | PPV, AMP |
| 2 | 1156 | 0.86 | 0.87 | 116 | GOL, PPV, AMP, SO4 |
| 3 | 832 | 0.85 | 0.88 | 85 | GOL, PPV, AMP, SO4 |
| 4 | 1010 | 0.85 | 0.86 | 93 | PPV, AMP, SO4, MG |
| 5 | 1033 | 0.85 | 0.86 | 94 | PPV, AMP |
Interfaces
6 interfaces between chains.
- D–E · 2149 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2148 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 482 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7TGL · Crystal structure of AMP+PPi bound DesD, the desferrioxamine synthetase from the… · the same entry in another collection · chain A against A, 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 7TGL · PDBe 7TGL
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