Research workbench
Crystal structure of the C707S mutant of C-terminal domain of 10'FORMYLTETRAHYDROFOLATE dehydrogenase in complex with NADP
Analyse Crystal structure of the C707S mutant of C-terminal domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GNZ
- Type
- protein
- Length
- 1,992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic 10-formyltetrahydrofolate dehydrogenase
- EC
- 1.5.1.6
- UniProt
- P28037
- Ligands
- NAP, SO4
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytosolic 10-formyltetrahydrofolate dehydrogenase (EC 1.5.1.6) | protein | 498 | 42% helix, 23% strand | P28037 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 28 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.85 | 0.92 | 57 | SO4 |
| 2 | 360 | 0.83 | 0.92 | 41 | SO4 |
| 3 | 395 | 0.81 | 0.90 | 36 | SO4 |
| 4 | 711 | 0.81 | 0.85 | 60 | SO4 |
| 5 | 417 | 0.81 | 0.89 | 39 | SO4 |
Interfaces
6 interfaces between chains.
- C–D · 2581 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2562 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1276 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1270 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1145 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4GNZ · Crystal structure of the c707s mutant of c-terminal domain of 10'formyltetrahydrofolate… · the same entry in another collection · chain A against A, TM-score 1.00
- P28037 · AlphaFold monomer V2.0 prediction for cytosolic 10-formyltetrahydrofolate dehydrogenase… · a predicted model of the same protein · chain C 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 P28037
- Elsewhere: RCSB PDB 4GNZ · PDBe 4GNZ · UniProt P28037
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