Research workbench
Human methylenetetrahydrofolate dehydrogenase / cyclohydrolase complexed with NADP and inhibitor LY249543
Analyse Human methylenetetrahydrofolate dehydrogenase / cyclohydrolase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DIA
- Type
- protein
- Length
- 580 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
- UniProt
- P11586
- Ligands
- NAP, L24
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE (EC 1.5.1.5, 3.5.4.9) | protein | 285 | 42% helix, 16% strand | P11586 |
| B | Methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE (EC 1.5.1.5, 3.5.4.9) | protein | 295 | 40% helix, 17% strand | P11586 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- L24 · [[[2-amino-5,6,7,8-tetrahydro-4-hydroxy-pyrido[2,3-d]pyrimidin-6-yl]-ethyl]-phenyl]-carbonyl-glutamic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.66 | 0.78 | 50 | NAP, L24 |
| 2 | 338 | 0.59 | 0.76 | 44 | NAP |
| 3 | 62 | 0.49 | 0.85 | 19 | empty |
| 4 | 64 | 0.43 | 0.82 | 19 | empty |
| 5 | 65 | 0.31 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1412 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1DIA · Human methylenetetrahydrofolate dehydrogenase / cyclohydrolase complexed with NADP and… · the same entry in another collection · chain B against B, 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 1DIA · PDBe 1DIA · UniProt P11586
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