Research workbench
The structure of the SER128ALA point-mutant variant of cysg, the multifunctional METHYLTRANSFERASE/DEHYDROGENASE/FERROCHELATASE for siroheme synthesis
Analyse The structure of the SER128ALA point-mutant variant of cysg, the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJT
- Type
- protein
- Length
- 903 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Siroheme synthase
- EC
- 2.1.1.107, 1.-.-.-, 4.99.1.-
- UniProt
- P25924
- Ligands
- SAH, PO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Siroheme synthase (EC 2.1.1.107, 1.-.-.-, 4.99.1.-) | protein | 448 | 38% helix, 21% strand | P25924 |
| B | Siroheme synthase (EC 2.1.1.107, 1.-.-.-, 4.99.1.-) | protein | 455 | 38% helix, 21% strand | P25924 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.72 | 0.80 | 43 | PO4 |
| 2 | 280 | 0.72 | 0.85 | 32 | empty |
| 3 | 554 | 0.69 | 0.79 | 51 | SAH |
| 4 | 494 | 0.68 | 0.79 | 56 | SAH |
| 5 | 348 | 0.66 | 0.81 | 58 | empty |
Interfaces
1 interface between chains.
- A–B · 6329 Ų buried · 96 hydrogen bonds · protein-protein
Compared structures
- 1PJT · The structure of the Ser128Ala point-mutant variant of CysG, the multifunctional… · the same entry in another collection · chain A against A, TM-score 1.00
- P25924 · AlphaFold monomer V2.0 prediction for siroheme synthase (P25924) · a predicted model of the same protein · chain B 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 P25924
- Elsewhere: RCSB PDB 1PJT · PDBe 1PJT · UniProt P25924
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