MolNFT v1 · #188198 · protein
Crystal structure of desd, the desferrioxamine synthetase from the streptomyces violaceus salmycin biosynthetic pathway
7TGN · Desferrioxamine synthetase desd: “Crystal structure of desd, the desferrioxamine synthetase from the streptomyces violaceus salmycin…”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.82). MolNFT v1 #188198 on…
- PDB
- 7TGN
- Type
- protein
- Length
- 2,289 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desferrioxamine synthetase desd
- Ligands
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desferrioxamine synthetase desd | protein | 575 | 44% helix, 20% strand | — |
| B | Desferrioxamine synthetase desd | protein | 576 | 45% helix, 19% strand | — |
| C | Desferrioxamine synthetase desd | protein | 568 | 43% helix, 19% strand | — |
| D | Desferrioxamine synthetase desd | protein | 570 | 45% helix, 19% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, C, B, D
- FLC · Citrate anion · additive · chains B
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 | 1004 | 0.82 | 0.83 | 86 | empty |
| 2 | 1066 | 0.81 | 0.82 | 84 | empty |
| 3 | 567 | 0.77 | 0.84 | 52 | empty |
| 4 | 576 | 0.75 | 0.82 | 50 | empty |
| 5 | 744 | 0.73 | 0.79 | 70 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2184 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2164 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 113 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 80 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7TGN · Crystal structure of DesD, the desferrioxamine synthetase from the Streptomyces violaceus… · 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 7TGN · PDBe 7TGN
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