MolNFT v1 · #134678 · protein
Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in complex with LY345899 and cofactors
5TC4 · Bifunctional methylenetetrahydrofolate…: “Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in…”. X-ray diffraction, 3 ligands (NAD, L34, PO4), 2 pockets (best druggability…
- PDB
- 5TC4
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- 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
- NAD, L34, PO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% 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 | 292 | 42% helix, 17% strand | P13995 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- L34 · 4-(7-amino-9-hydroxy-1-oxo-3,3A,4,5-tetrahydro-2,5,6,8,9B-pentaaza-cyclopenta[a]naphthalen-2-yl)-phenylcarbonyl-glutami C acid · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.68 | 0.78 | 57 | NAD, L34 |
| 2 | 100 | 0.38 | 0.74 | 18 | empty |
Compared structures
- 5TC4 · Crystal structure of human mitochondrial methylenetetrahydrofolate… · the same entry in another collection · chain A against A, TM-score 1.00
- P13995 · AlphaFold monomer V2.0 prediction for bifunctional methylenetetrahydrofolate… · a predicted model of the same protein · 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 P13995
- Elsewhere: RCSB PDB 5TC4 · PDBe 5TC4 · UniProt P13995
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