MolNFT v1 · #72707 · protein
Crystal structure of bifunctional 5,10-methylenetetrahydrofolate dehydrogenase / cyclohydrolase from thermoplasma acidophilum
3NGL · Bifunctional protein fold: “Crystal structure of bifunctional 5,10-methylenetetrahydrofolate dehydrogenase / cyclohydrolase from…”. X-ray diffraction, 1 ligand (NAP), 4 pockets (best druggability 0.65). MolNFT v1 #72707 on…
- PDB
- 3NGL
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein fold
- EC
- 1.5.1.5, 3.5.4.9
- UniProt
- Q05213
- Ligands
- NAP
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein fold (EC 1.5.1.5, 3.5.4.9) | protein | 275 | 44% helix, 17% strand | Q05213 |
| C | Bifunctional protein fold (EC 1.5.1.5, 3.5.4.9) | protein | 274 | 42% helix, 18% strand | Q05213 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.65 | 0.78 | 46 | NAP |
| 2 | 436 | 0.61 | 0.76 | 45 | NAP |
| 3 | 82 | 0.37 | 0.77 | 29 | empty |
| 4 | 69 | 0.30 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–C · 1592 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3NGL · Crystal structure of bifunctional 5,10-methylenetetrahydrofolate dehydrogenase /… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05213 · AlphaFold monomer V2.0 prediction for bifunctional protein fold (Q05213) · 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 Q05213
- Elsewhere: RCSB PDB 3NGL · PDBe 3NGL · UniProt Q05213
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