MolNFT v1 · #88144 · protein
Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor and inhibitor
4CM1: “Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor…”. X-ray diffraction, 2 ligands (NAP, IQW), 9 pockets (best druggability 0.83). MolNFT v1 #88144 on GenesisL1: 3D structure…
- PDB
- 4CM1
- Type
- protein
- Length
- 1,000 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, IQW
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase 1 (EC 1.5.1.33) | protein | 251 | 47% helix, 15% strand | O76290 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 249 | 47% helix, 15% strand | O76290 |
| C, D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 250 | 47% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- IQW · 5-(p-tolyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
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 | 1165 | 0.83 | 0.84 | 71 | empty |
| 2 | 645 | 0.76 | 0.82 | 51 | DTT, NAP, IQW |
| 3 | 641 | 0.76 | 0.82 | 48 | DTT, NAP, IQW |
| 4 | 638 | 0.76 | 0.82 | 50 | DTT, NAP, IQW |
| 5 | 590 | 0.75 | 0.82 | 46 | NAP, IQW |
Interfaces
6 interfaces between chains.
- B–D · 1890 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1863 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1401 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1400 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 556 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 4CM1 · 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 4CM1 · PDBe 4CM1 · UniProt O76290
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