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Pandda analysis group deposition -- crystal structure of trypanosoma brucei trypanothione reductase in complex with Z2856434884
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
- 5S9Z
- 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
- FAD, O3J, MG, BR
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% 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 | 34% helix, 27% 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
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- O3J · 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one · 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 · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.87 | 0.88 | 101 | empty |
| 2 | 782 | 0.80 | 0.83 | 99 | FAD, DMS |
| 3 | 716 | 0.79 | 0.83 | 94 | FAD |
| 4 | 104 | 0.52 | 0.83 | 24 | O3J |
| 5 | 51 | 0.50 | 0.88 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3432 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5S9Z · 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 5S9Z · PDBe 5S9Z · UniProt A0A3L6KZJ1
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