MolNFT v1 · #68250 · protein
Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6- phenylpteridine-2,4,7-triamine (DX2)
3JQ7: “Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor…”. X-ray diffraction, 2 ligands (NAP, DX2), 7 pockets (best druggability 0.83). MolNFT v1 #68250 on GenesisL1: 3D structure…
- PDB
- 3JQ7
- Type
- protein
- Length
- 984 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase 1
- EC
- 1.5.1.33
- UniProt
- Q581W1
- Ligands
- NAP, DX2
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 249 | 48% helix, 14% strand | Q581W1 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 247 | 48% helix, 15% strand | Q581W1 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 239 | 48% helix, 15% strand | Q581W1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- DX2 · 6-phenylpteridine-2,4,7-triamine · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.83 | 0.84 | 70 | empty |
| 2 | 652 | 0.77 | 0.82 | 51 | NAP, DX2 |
| 3 | 609 | 0.76 | 0.82 | 47 | NAP, DX2 |
| 4 | 616 | 0.76 | 0.82 | 46 | NAP, DX2, DTT |
| 5 | 569 | 0.74 | 0.82 | 45 | NAP, DX2 |
Interfaces
6 interfaces between chains.
- B–D · 1848 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1816 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1432 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1415 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 561 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (oxidation).
Compared structures
- 3JQ7 · 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 Q581W1
- Elsewhere: RCSB PDB 3JQ7 · PDBe 3JQ7 · UniProt Q581W1
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