MolNFT v1 · #106538 · protein
Crystal structure of caulobacter crescentus thic with FE4S4 cluster at remote site (holo form)
4S2A · Phosphomethylpyrimidine synthase: “Crystal structure of caulobacter crescentus thic with FE4S4 cluster at remote site (holo form)”. X-ray diffraction, 2 ligands (SF4, PO4), 6 pockets (best druggability 0.67). MolNFT v1 #106538 on…
- PDB
- 4S2A
- Type
- protein
- Length
- 594 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine synthase
- EC
- 4.1.99.17
- UniProt
- Q9A6Q5
- Ligands
- SF4, PO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylpyrimidine synthase (EC 4.1.99.17) | protein | 594 | 41% helix, 11% strand | Q9A6Q5 |
Ligands and binding sites
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 | 435 | 0.67 | 0.79 | 43 | PO4 |
| 2 | 173 | 0.66 | 0.86 | 31 | empty |
| 3 | 80 | 0.53 | 0.85 | 20 | empty |
| 4 | 111 | 0.43 | 0.77 | 17 | empty |
| 5 | 80 | 0.31 | 0.73 | 18 | empty |
Compared structures
- 4S2A · Crystal structure of Caulobacter crescentus ThiC with Fe4S4 cluster at remote site (holo… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9A6Q5 · AlphaFold monomer V2.0 prediction for phosphomethylpyrimidine synthase (Q9A6Q5) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9A6Q5
- Elsewhere: RCSB PDB 4S2A · PDBe 4S2A · UniProt Q9A6Q5
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