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The co-crystal structure of cysg, the multifunctional METHYLTRANSFERASE/DEHYDROGENASE/FERROCHELATASE for siroheme synthesis, in complex with it NAD cofactor
Analyse The co-crystal structure of cysg, the multifunctional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJS
- Type
- protein
- Length
- 897 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, NAD, PO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Siroheme synthase (EC 2.1.1.107, 1.-.-.-, 4.99.1.-) | protein | 443 | 38% helix, 23% strand | P25924 |
| B | Siroheme synthase (EC 2.1.1.107, 1.-.-.-, 4.99.1.-) | protein | 454 | 38% helix, 22% strand | P25924 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.75 | 0.78 | 113 | PGE, PO4 |
| 2 | 323 | 0.72 | 0.85 | 43 | PGE |
| 3 | 475 | 0.69 | 0.79 | 52 | SAH |
| 4 | 398 | 0.66 | 0.80 | 47 | SAH |
| 5 | 226 | 0.57 | 0.79 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 6417 Ų buried · 96 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
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 1PJS · PDBe 1PJS · UniProt P25924
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