MolNFT v1 · #177402 · protein
Human MTHFD2 in complex with compound 21, cofactor and phosphate.
7EHJ · Bifunctional methylenetetrahydrofolate…: “Human MTHFD2 in complex with compound 21, cofactor and phosphate.”. X-ray diffraction, 3 ligands (J49, NAD, PO4), 7 pockets (best druggability 0.67). MolNFT v1 #177402 on GenesisL1: 3D…
- PDB
- 7EHJ
- Type
- protein
- Length
- 580 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
- J49, NAD, PO4
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 290 | 42% helix, 16% strand | P13995 |
Ligands and binding sites
- J49 · (2S)-2-[[4-[(4-azanyl-6-oxidanyl-pyrimidin-5-yl) carbamoylamino]phenyl]carbonylamino]pentanedioic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.67 | 0.79 | 50 | J49, NAD |
| 2 | 470 | 0.66 | 0.78 | 50 | J49, NAD |
| 3 | 196 | 0.48 | 0.75 | 33 | PO4 |
| 4 | 150 | 0.48 | 0.77 | 32 | empty |
| 5 | 172 | 0.46 | 0.75 | 28 | PO4, NAD |
Interfaces
1 interface between chains.
- A–B · 1664 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7EHJ · human MTHFD2 in complex with compound 21, cofactor and phosphate. · 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 0.99
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 7EHJ · PDBe 7EHJ · UniProt P13995
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.