Research workbench
High resolution structure of TBPTR1 in complex with cyromazine
Analyse High resolution structure of TBPTR1 in complex with cyromazine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X9N
- Type
- protein
- Length
- 992 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, AX3, D1D, NA
- 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, B | Pteridine reductase (EC 1.5.1.33) | protein | 248 | 48% helix, 15% strand | O76290 |
| C | Pteridine reductase (EC 1.5.1.33) | protein | 249 | 47% helix, 15% strand | O76290 |
| D | Pteridine reductase (EC 1.5.1.33) | protein | 247 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- AX3 · N~2~-cyclopropyl-1,3,5-triazine-2,4,6-triamine · ligand · 4 copies · chains A, B, C, D
- D1D · (4S,5S)-1,2-dithiane-4,5-diol · ligand · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains A, D
- DTD · Dithiane diol · additive · 2 copies · chains A, C
- ACT · Acetate ion · additive · chains 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 | 1170 | 0.83 | 0.84 | 70 | empty |
| 2 | 594 | 0.77 | 0.83 | 48 | NAP, AX3, D1D |
| 3 | 613 | 0.77 | 0.83 | 46 | NAP, AX3, DTD |
| 4 | 650 | 0.77 | 0.82 | 60 | NAP, AX3, D1D |
| 5 | 576 | 0.75 | 0.82 | 47 | NAP, AX3, DTD |
Interfaces
6 interfaces between chains.
- C–D · 1866 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1822 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1393 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1392 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 561 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2X9N · High resolution structure of TbPTR1 in complex with cyromazine · 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 2X9N · PDBe 2X9N · UniProt O76290
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