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Structure of human MTHFD2 in complex with TH9619
Analyse Structure of human MTHFD2 in complex with TH9619 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S4F
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial
- EC
- 1.5.1.15, 3.5.4.9
- UniProt
- P13995
- Ligands
- KUN, ADP, PO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 289 | 42% helix, 15% strand | P13995 |
| B | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 298 | 40% helix, 17% strand | P13995 |
Ligands and binding sites
- KUN · (E,4S)-4-[[5-[2-[2,6-bis(azanyl)-4-oxidanylidene-1H-pyrimidin-5-yl]ethanoylamino]-3-fluoranyl-pyridin-2-yl]carbonylamino]pent-2-enedioic acid · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- PO4 · Phosphate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.74 | 0.99 | 14 | empty |
| 2 | 592 | 0.69 | 0.78 | 63 | KUN, ADP |
| 3 | 485 | 0.67 | 0.79 | 51 | KUN |
| 4 | 202 | 0.53 | 0.77 | 22 | GOL |
| 5 | 190 | 0.48 | 0.75 | 35 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1621 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
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 P13995
- Elsewhere: RCSB PDB 6S4F · PDBe 6S4F · UniProt P13995
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