MolNFT v1 · #163248 · protein
Trypanosoma brucei PTR1 (TBPTR1) in complex with inhibitor 1 (nmt- C0003)
6RX5 · Pteridine reductase: “Trypanosoma brucei PTR1 (TBPTR1) in complex with inhibitor 1 (nmt- C0003)”. X-ray diffraction, 2 ligands (NAP, FE1), 9 pockets (best druggability 0.83). MolNFT v1 #163248 on GenesisL1: 3D structure, binding…
- PDB
- 6RX5
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, FE1
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase | protein | 258 | 46% helix, 14% strand | O76290 |
| B | Pteridine reductase | protein | 247 | 48% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 233 | 49% helix, 16% strand | O76290 |
| D | Pteridine reductase | 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
- FE1 · Methyl 1-(4-{[(2,4-diaminopteridin-6-yl) methyl](methyl)amino}benzoyl)piperidine-4-carboxylate · ligand · 3 copies · chains A, B, D
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.83 | 0.84 | 70 | empty |
| 2 | 632 | 0.77 | 0.82 | 49 | NAP, FE1 |
| 3 | 624 | 0.76 | 0.82 | 50 | NAP, FE1 |
| 4 | 608 | 0.75 | 0.82 | 47 | NAP, FE1 |
| 5 | 495 | 0.66 | 0.77 | 52 | NAP |
Interfaces
6 interfaces between chains.
- A–C · 1866 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1858 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1463 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1395 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6RX5 · Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 1 (NMT-C0003) · 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 6RX5 · PDBe 6RX5 · UniProt O76290
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