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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
Analyse Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CM9
- Type
- protein
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- TRYPANOSOMA BRUCEI BRUCEI
- Molecule
- Pteridine reductase 1
- EC
- 1.5.1.33
- UniProt
- O76290
- Ligands
- NAP, YGL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 249 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- YGL · 2-amino-5,6-diphenyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one · ligand · 4 copies · chains A, B, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains A, D, B, C
- ACT · Acetate ion · additive · chains C, D
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 | 1175 | 0.83 | 0.84 | 73 | ACT |
| 2 | 633 | 0.78 | 0.83 | 52 | NAP, YGL |
| 3 | 590 | 0.76 | 0.83 | 50 | DTT, NAP, YGL |
| 4 | 607 | 0.76 | 0.82 | 49 | DTT, NAP, YGL |
| 5 | 597 | 0.76 | 0.82 | 51 | DTT, NAP, YGL |
Interfaces
6 interfaces between chains.
- B–D · 1838 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1830 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1404 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 565 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 modified (additive adduct, oxidation).
Compared structures
- 4CM9 · Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary… · 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 O76290
- Elsewhere: RCSB PDB 4CM9 · PDBe 4CM9 · UniProt O76290
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