MolNFT v1 · #162503 · protein
Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6- DIMETHYLBICYCLO[3.1.1]HEPTAN-2-YL)ETHYL)-4-oxo-1-phenyl-1,3,8- TRIAZASPIRO[4.5]DECAN-3-YL)PROPYL)(METHYL)AMINO)METHYL)-4- hydroxypiperidine-1-carboximidamide
6RB5: “Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6…”. X-ray diffraction, 3 ligands (JWZ, FAD, SO4), 9 pockets (best druggability 0.86). MolNFT v1 #162503 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6RB5
- Type
- protein
- Length
- 979 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypanothione reductase
- EC
- 1.8.1.12
- UniProt
- Q389T8
- Ligands
- JWZ, FAD, SO4
- 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 | Trypanothione reductase (EC 1.8.1.12) | protein | 490 | 33% helix, 27% strand | Q389T8 |
| B | Trypanothione reductase (EC 1.8.1.12) | protein | 489 | 33% helix, 28% strand | Q389T8 |
Ligands and binding sites
- JWZ · 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl) (methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.86 | 0.88 | 73 | GOL |
| 2 | 895 | 0.81 | 0.83 | 104 | FAD, SO4 |
| 3 | 901 | 0.80 | 0.82 | 101 | FAD, SO4, GOL |
| 4 | 128 | 0.56 | 0.83 | 27 | empty |
| 5 | 84 | 0.48 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3409 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6RB5 · Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1… · 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 Q389T8
- Elsewhere: RCSB PDB 6RB5 · PDBe 6RB5 · UniProt Q389T8
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