Research workbench
The crystal structure of trypanosoma brucei N5, N10- methylenetetrahydrofolate dehydrogenase-cyclohydrolase (fold) complexed with NADP cofactor and inhibitor
Analyse The crystal structure of trypanosoma brucei N5, N10- methylenetetrahydrofolate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CJX
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-1-tetrahydrofolate synthase, cytoplasmic, putative
- EC
- 1.5.1.5
- UniProt
- Q57WP0
- Ligands
- 9L9, NAP
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-1-tetrahydrofolate synthase, cytoplasmic, putative (EC 1.5.1.5) | protein | 297 | 42% helix, 17% strand | Q57WP0 |
Ligands and binding sites
- 9L9 · (2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.81 | 0.89 | 55 | PEG |
| 2 | 656 | 0.72 | 0.79 | 69 | 9L9, NAP |
| 3 | 618 | 0.71 | 0.79 | 63 | 9L9 |
| 4 | 108 | 0.47 | 0.79 | 24 | empty |
| 5 | 175 | 0.45 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1356 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4CJX · The crystal structure of Trypanosoma brucei N5, N10- methylenetetrahydrofolate… · 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 Q57WP0
- Elsewhere: RCSB PDB 4CJX · PDBe 4CJX · UniProt Q57WP0
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