Research workbench
Crystal structure of arabidopsis thaliana thic with bound imidazole ribonucleotide, S-adenosylhomocysteine, FE4S4 cluster and zn (monoclinic crystal form)
Analyse Crystal structure of arabidopsis thaliana thic with bound imidazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S26
- Type
- protein
- Length
- 1,031 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine synthase, chloroplastic
- EC
- 4.1.99.17
- UniProt
- O82392
- Ligands
- SF4, IRN, SAH, ZN, CL
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylpyrimidine synthase, chloroplastic (EC 4.1.99.17) | protein | 519 | 47% helix, 12% strand | O82392 |
| B | Phosphomethylpyrimidine synthase, chloroplastic (EC 4.1.99.17) | protein | 512 | 47% helix, 12% strand | O82392 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- IRN · 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.87 | 0.95 | 50 | SF4, CL, IRN, SAH, ZN |
| 2 | 374 | 0.87 | 0.95 | 52 | IRN, SAH, ZN, CL, SF4 |
| 3 | 230 | 0.73 | 0.88 | 40 | empty |
| 4 | 189 | 0.67 | 0.86 | 29 | empty |
| 5 | 107 | 0.57 | 0.85 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 4650 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4S26 · Crystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide… · the same entry in another collection · chain A against A, TM-score 1.00
- O82392 · AlphaFold monomer V2.0 prediction for phosphomethylpyrimidine synthase, chloroplastic… · a predicted model of the same protein · chain B 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 O82392
- Elsewhere: RCSB PDB 4S26 · PDBe 4S26 · UniProt O82392
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