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Structure of trypanosoma brucei pteridine reductase (PTR1) in ternary complex with cofactor and the antifolate methotrexate
Analyse Structure of trypanosoma brucei pteridine reductase (PTR1) in ternary complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C7V
- Type
- protein
- Length
- 1,024 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, MTX, NI
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase (EC 1.5.1.33) | protein | 253 | 47% helix, 15% strand | O76290 |
| B | Pteridine reductase (EC 1.5.1.33) | protein | 254 | 48% helix, 14% strand | O76290 |
| C | Pteridine reductase (EC 1.5.1.33) | protein | 260 | 46% helix, 13% strand | O76290 |
| D | Pteridine reductase (EC 1.5.1.33) | protein | 257 | 46% helix, 14% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MTX · Methotrexate · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, C, B, D
- 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.83 | 0.84 | 69 | NI |
| 2 | 570 | 0.75 | 0.82 | 40 | NAP, MTX |
| 3 | 561 | 0.75 | 0.82 | 43 | NAP, MTX |
| 4 | 632 | 0.74 | 0.81 | 61 | NAP, MTX |
| 5 | 526 | 0.74 | 0.82 | 40 | NAP, MTX |
Interfaces
6 interfaces between chains.
- A–C · 1962 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1899 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1454 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1432 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 564 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 2C7V · Structure of Trypanosoma brucei pteridine reductase (PTR1) in ternary complex with… · the same entry in another collection · chain B against B, 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 2C7V · PDBe 2C7V · UniProt O76290
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