Research workbench
Crystal structure of hsc-ams bound desd, the desferrioxamine synthetase from the streptomyces griseoflavus ferrimycin biosynthetic pathway
Analyse Crystal structure of hsc-ams 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
- 7TGM
- Type
- protein
- Length
- 2,960 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desferrioxamine synthetase desd
- Ligands
- I3U, LMS, MG, SO4, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desferrioxamine synthetase desd | protein | 593 | 42% helix, 21% strand | — |
| B, C, D | Desferrioxamine synthetase desd | protein | 592 | 42% helix, 21% strand | — |
| E | Desferrioxamine synthetase desd | protein | 591 | 42% helix, 21% strand | — |
Ligands and binding sites
- I3U · 4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic acid · ligand · 5 copies · chains A, B, C, E, D
- LMS · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl sulfamate · ligand · 5 copies · chains A, B, C, E, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, E, D
- SO4 · Sulfate ion · ion · 47 copies · chains A, C, D, B, E
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, E, D
- GOL · Glycerol · additive · 59 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.88 | 0.89 | 114 | GOL, I3U, LMS, PO4, MG, SO4 |
| 2 | 808 | 0.88 | 0.91 | 110 | GOL, I3U, LMS, PO4, MG |
| 3 | 1077 | 0.87 | 0.89 | 118 | GOL, I3U, LMS, PO4, MG |
| 4 | 1068 | 0.87 | 0.88 | 102 | GOL, I3U, LMS, PO4, MG |
| 5 | 1122 | 0.86 | 0.87 | 107 | I3U, LMS, PO4, MG, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 2151 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 2146 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 545 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7TGM · Crystal structure of HSC-AMS 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 7TGM · PDBe 7TGM
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