MolNFT v1 · #88116 · protein
Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor and inhibitor
4CL8: “Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor…”. X-ray diffraction, 2 ligands (OZJ, NAP), 7 pockets (best druggability 0.83). MolNFT v1 #88116 on GenesisL1: 3D structure…
- PDB
- 4CL8
- Type
- protein
- Length
- 1,001 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
- O76290
- Ligands
- OZJ, NAP
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 251 | 47% helix, 15% strand | O76290 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 248 | 47% helix, 15% strand | O76290 |
Ligands and binding sites
- OZJ · 2,4-diamino-6-(3-formylphenyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C
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 | 1160 | 0.83 | 0.84 | 72 | empty |
| 2 | 623 | 0.77 | 0.83 | 46 | OZJ, NAP, ACT |
| 3 | 632 | 0.77 | 0.83 | 53 | OZJ, NAP |
| 4 | 610 | 0.77 | 0.83 | 50 | OZJ, NAP |
| 5 | 571 | 0.76 | 0.83 | 47 | OZJ, NAP, ACT |
Interfaces
6 interfaces between chains.
- B–D · 1891 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1870 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1404 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1400 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 566 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4CL8 · 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 4CL8 · PDBe 4CL8 · UniProt O76290
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