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Crystal structure of arabidopsis thaliana thic with bound aminoimidazole ribonucleotide, 5'-deoxyadenosine, L-methionine, FE4S4 cluster and fe
Analyse Crystal structure of arabidopsis thaliana thic with bound aminoimidazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S27
- Type
- protein
- Length
- 514 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, AIR, 5AD, MET, FE2, CL
- Pockets
- 6 · best druggability 0.76
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 | 514 | 46% helix, 12% strand | O82392 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- AIR · 5-aminoimidazole ribonucleotide · ligand · chains A
- 5AD · 5'-deoxyadenosine · ligand · chains A
- MET · Methionine · ligand · chains A
- FE2 · Fe (II) 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.76 | 0.88 | 41 | BU1 |
| 2 | 363 | 0.74 | 0.85 | 41 | AIR, 5AD, MET, FE2 |
| 3 | 97 | 0.59 | 0.87 | 27 | empty |
| 4 | 98 | 0.36 | 0.74 | 17 | empty |
| 5 | 60 | 0.33 | 0.76 | 15 | empty |
Compared structures
- 4S27 · Crystal structure of Arabidopsis thaliana ThiC with bound aminoimidazole 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 4S27 · PDBe 4S27 · UniProt O82392
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