MolNFT v1 · #188194 · protein
Crystal structure of desd, the desferrioxamine synthetase from the streptomyces griseoflavus ferrimycin biosynthetic pathway
7TGJ · Desferrioxamine synthetase desd: “Crystal structure of desd, the desferrioxamine synthetase from the streptomyces griseoflavus ferrimycin…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.83). MolNFT v1 #188194…
- PDB
- 7TGJ
- Type
- protein
- Length
- 2,900 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desferrioxamine synthetase desd
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desferrioxamine synthetase desd | protein | 580 | 45% helix, 20% strand | — |
| B | Desferrioxamine synthetase desd | protein | 580 | 45% helix, 20% strand | — |
| C | Desferrioxamine synthetase desd | protein | 580 | 41% helix, 20% strand | — |
| D | Desferrioxamine synthetase desd | protein | 579 | 44% helix, 20% strand | — |
| E | Desferrioxamine synthetase desd | protein | 581 | 43% helix, 20% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 27 copies · chains A, B, C, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.83 | 0.84 | 98 | SO4 |
| 2 | 871 | 0.82 | 0.84 | 86 | SO4 |
| 3 | 916 | 0.82 | 0.84 | 98 | SO4 |
| 4 | 1177 | 0.81 | 0.82 | 103 | SO4 |
| 5 | 1088 | 0.81 | 0.82 | 114 | SO4 |
Interfaces
7 interfaces between chains.
- C–D · 2152 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2139 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 454 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 450 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 426 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7TGJ · Crystal structure of DesD, the desferrioxamine synthetase from the Streptomyces… · 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 7TGJ · PDBe 7TGJ
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