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Crystal structure of a hydrogen sulfide-producing enzyme (FN1220) from fusobacterium nucleatum in complex with L-serine-plp schiff base
Analyse Crystal structure of a hydrogen sulfide-producing enzyme (FN1220) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XEN
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine synthase
- EC
- 2.5.1.47
- UniProt
- Q8RE94
- Ligands
- PLP, SER, CA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine synthase (EC 2.5.1.47) | protein | 300 | 44% helix, 18% strand | Q8RE94 |
| B | Cysteine synthase (EC 2.5.1.47) | protein | 301 | 44% helix, 18% strand | Q8RE94 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B
- SER · Serine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
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 | 342 | 0.75 | 0.86 | 67 | empty |
| 2 | 212 | 0.71 | 0.88 | 47 | PLP, SER |
| 3 | 213 | 0.70 | 0.87 | 47 | PLP, SER, ACT |
| 4 | 95 | 0.47 | 0.80 | 15 | empty |
| 5 | 75 | 0.38 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1637 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5XEN · Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium… · the same entry in another collection · 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 Q8RE94
- Elsewhere: RCSB PDB 5XEN · PDBe 5XEN · UniProt Q8RE94
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