MolNFT v1 · #88161 · protein
Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor and inhibitor
4CMI: “Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor…”. X-ray diffraction, 2 ligands (NAP, M4V), 9 pockets (best druggability 0.84). MolNFT v1 #88161 on GenesisL1: 3D structure…
- PDB
- 4CMI
- 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
- NAP, M4V
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 250 | 47% helix, 15% strand | O76290 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 251 | 48% helix, 16% strand | O76290 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 250 | 47% helix, 14% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- M4V · 2-amino-6-(4-bromophenyl)-5-phenyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one · ligand · 4 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 2 copies · chains B, C
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 | 1170 | 0.84 | 0.85 | 68 | empty |
| 2 | 648 | 0.78 | 0.83 | 50 | NAP, M4V |
| 3 | 613 | 0.78 | 0.83 | 48 | NAP, M4V |
| 4 | 632 | 0.78 | 0.83 | 48 | NAP, M4V |
| 5 | 589 | 0.75 | 0.82 | 47 | NAP, M4V |
Interfaces
6 interfaces between chains.
- A–C · 1859 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1857 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1391 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1385 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4CMI · 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 4CMI · PDBe 4CMI · UniProt O76290
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