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Crystal structure of N10-formyltetrahydrofolate synthetase with ZD9331, formylphosphate, and ADP
Analyse Crystal structure of N10-formyltetrahydrofolate synthetase with ZD9331… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JKI
- Type
- protein
- Length
- 1,112 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate--tetrahydrofolate ligase
- EC
- 6.3.4.3
- UniProt
- Q2RM91
- Ligands
- ZD9, XPO, ADP, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate--tetrahydrofolate ligase (EC 6.3.4.3) | protein | 557 | 39% helix, 18% strand | Q2RM91 |
| B | Formate--tetrahydrofolate ligase (EC 6.3.4.3) | protein | 555 | 39% helix, 18% strand | Q2RM91 |
Ligands and binding sites
- ZD9 · 2,7-dimethyl-6-[(prop-1-yn-1-ylamino)methyl]quinazolin-4(3H)-one · ligand · chains A
- XPO · formyl phosphate · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.76 | 0.79 | 116 | empty |
| 2 | 871 | 0.71 | 0.76 | 68 | ZD9, XPO, ADP, SO4 |
| 3 | 718 | 0.68 | 0.76 | 56 | SO4 |
| 4 | 266 | 0.68 | 0.84 | 40 | empty |
| 5 | 279 | 0.67 | 0.83 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 3031 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4JKI · Crystal Structure of N10-Formyltetrahydrofolate Synthetase with ZD9331, Formylphosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2RM91 · AlphaFold monomer V2.0 prediction for formate--tetrahydrofolate ligase (Q2RM91) · 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 Q2RM91
- Elsewhere: RCSB PDB 4JKI · PDBe 4JKI · UniProt Q2RM91
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