MolNFT v1 · #52375 · protein
Pteridine reductase 1 (PTR1) from trypanosoma brucei in complex with NADP and DDD00066641
2VZ0: “Pteridine reductase 1 (PTR1) from trypanosoma brucei in complex with NADP and DDD00066641”. X-ray diffraction, 2 ligands (NAP, D64), 8 pockets (best druggability 0.83). MolNFT v1 #52375 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VZ0
- Type
- protein
- Length
- 995 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- EC
- 1.5.1.33
- UniProt
- O76290
- Ligands
- NAP, D64
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Pteridine reductase (EC 1.5.1.33) | protein | 249 | 48% helix, 14% strand | O76290 |
| B | Pteridine reductase (EC 1.5.1.33) | protein | 248 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- D64 · 6-(4-methylphenyl)quinazoline-2,4-diamine · ligand · 4 copies · chains A, B, 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 | 1158 | 0.83 | 0.84 | 70 | empty |
| 2 | 647 | 0.77 | 0.82 | 48 | NAP, D64 |
| 3 | 666 | 0.76 | 0.82 | 48 | NAP, D64 |
| 4 | 639 | 0.76 | 0.81 | 50 | NAP, D64 |
| 5 | 614 | 0.75 | 0.82 | 47 | NAP, D64 |
Interfaces
6 interfaces between chains.
- A–C · 1834 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1826 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1440 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 553 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VZ0 · Pteridine Reductase 1 (PTR1) from Trypanosoma Brucei in complex with NADP and DDD00066641 · 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 2VZ0 · PDBe 2VZ0 · UniProt O76290
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