MolNFT v1 · #147427 · protein
The human methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE (fold) complexed with NADP and inhibitor LY249543
6ECP · Methylenetetrahydrofolate dehydrogenase cyclohydrolase: “The human methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE (fold) complexed with NADP and inhibitor…”. X-ray diffraction, 1 ligand (NAP), 5 pockets (best druggability…
- PDB
- 6ECP
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylenetetrahydrofolate dehydrogenase cyclohydrolase
- EC
- 1.5.1.5, 3.5.4.9, 6.3.4.3
- UniProt
- P11586
- Ligands
- NAP
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylenetetrahydrofolate dehydrogenase cyclohydrolase (EC 1.5.1.5, 3.5.4.9, 6.3.4.3) | protein | 289 | 44% helix, 16% strand | P11586 |
| B | Methylenetetrahydrofolate dehydrogenase cyclohydrolase (EC 1.5.1.5, 3.5.4.9, 6.3.4.3) | protein | 295 | 41% helix, 17% strand | P11586 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.59 | 0.81 | 35 | NAP |
| 2 | 300 | 0.56 | 0.76 | 33 | NAP |
| 3 | 69 | 0.55 | 0.87 | 22 | empty |
| 4 | 67 | 0.44 | 0.82 | 17 | empty |
| 5 | 139 | 0.43 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1406 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6ECP · The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P11586 · AlphaFold monomer V2.0 prediction for C-1-tetrahydrofolate synthase, cytoplasmic (P11586) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P11586
- Elsewhere: RCSB PDB 6ECP · PDBe 6ECP · UniProt P11586
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