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Crystal structure of hydrogen sulfide-producing enzyme (FN1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine- dimethylated form
Analyse Crystal structure of hydrogen sulfide-producing enzyme (FN1055) D232N mutant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B55
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine synthase
- EC
- 2.5.1.47
- UniProt
- Q8REP3
- Ligands
- PLP, 0JO
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine synthase (EC 2.5.1.47) | protein | 334 | 41% helix, 20% strand | Q8REP3 |
| B | Cysteine synthase (EC 2.5.1.47) | protein | 333 | 41% helix, 20% strand | Q8REP3 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 31 | PLP, 0JO |
| 2 | 69 | 0.73 | 0.98 | 29 | PLP, 0JO |
| 3 | 133 | 0.51 | 0.80 | 23 | PEG |
| 4 | 84 | 0.49 | 0.83 | 25 | empty |
| 5 | 98 | 0.47 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1896 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified, 2 cofactor (methylation, pyridoxal phosphate Schiff base).
Compared structures
- 5B55 · Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed… · the same entry in another collection · chain B against B, 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 Q8REP3
- Elsewhere: RCSB PDB 5B55 · PDBe 5B55 · UniProt Q8REP3
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