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Crystal structure of arabidopsis thaliana thic with bound imidazole ribonucleotide, S-adenosylhomocysteine, FE4S4 cluster and zn (trigonal 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
- 4S25
- Type
- protein
- Length
- 513 residues
- Chains
- 1
- 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
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylpyrimidine synthase, chloroplastic (EC 4.1.99.17) | protein | 513 | 46% helix, 12% strand | O82392 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- IRN · 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- BU1 · 1,4-butanediol · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.74 | 0.85 | 44 | IRN, SAH, ZN |
| 2 | 61 | 0.70 | 0.97 | 18 | empty |
| 3 | 209 | 0.68 | 0.86 | 29 | BU1 |
| 4 | 99 | 0.57 | 0.85 | 29 | empty |
| 5 | 152 | 0.42 | 0.74 | 29 | SF4, CL |
Compared structures
- 4S25 · 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 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 O82392
- Elsewhere: RCSB PDB 4S25 · PDBe 4S25 · UniProt O82392
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