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Pandda analysis group deposition -- crystal structure of trypanosoma brucei trypanothione reductase in complex with Z1506050651
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
- 5SA0
- Type
- protein
- Length
- 968 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, NXJ, MG, BR
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% 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 | 485 | 33% helix, 27% strand | A0A3L6KZJ1 |
| B | N(1),N(8)-BIS(GLUTATHIONYL)SPERMIDINE reductase (EC 1.8.1.12) | protein | 483 | 33% helix, 28% strand | A0A3L6KZJ1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NXJ · (1S)-N,2,2-trimethyl-N-(pyridin-3-yl)cyclopropane-1-carboxamide · 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 · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.86 | 0.89 | 74 | empty |
| 2 | 716 | 0.80 | 0.83 | 100 | FAD, NXJ |
| 3 | 780 | 0.79 | 0.83 | 99 | FAD, NXJ |
| 4 | 181 | 0.62 | 0.84 | 29 | empty |
| 5 | 110 | 0.54 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3450 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5SA0 · 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 5SA0 · PDBe 5SA0 · UniProt A0A3L6KZJ1
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