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Pandda analysis group deposition -- crystal structure of trypanosoma brucei trypanothione reductase in complex with Z1899842917
Analyse Pandda analysis group deposition -- crystal structure of trypanosoma brucei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5S9X
- Type
- protein
- Length
- 969 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N(1),N(8)-BIS(GLUTATHIONYL)SPERMIDINE reductase
- EC
- 1.8.1.12
- UniProt
- A0A3L6KZJ1
- Ligands
- K1A, FAD, MG, BR
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N(1),N(8)-BIS(GLUTATHIONYL)SPERMIDINE reductase (EC 1.8.1.12) | protein | 486 | 33% helix, 28% strand | A0A3L6KZJ1 |
| B | N(1),N(8)-BIS(GLUTATHIONYL)SPERMIDINE reductase (EC 1.8.1.12) | protein | 483 | 34% helix, 28% strand | A0A3L6KZJ1 |
Ligands and binding sites
- K1A · 3-[(3,5-dimethyl-1,2-oxazol-4-yl)methyl]-5-methyl-1,3,4-thiadiazol-2(3H)-one · ligand · 3 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.86 | 0.89 | 72 | empty |
| 2 | 755 | 0.79 | 0.83 | 94 | FAD, K1A |
| 3 | 94 | 0.79 | 0.99 | 20 | K1A |
| 4 | 756 | 0.79 | 0.82 | 99 | FAD, K1A |
| 5 | 119 | 0.56 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3344 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5S9X · PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione… · 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
- Every structure of UniProt A0A3L6KZJ1
- Elsewhere: RCSB PDB 5S9X · PDBe 5S9X · UniProt A0A3L6KZJ1
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