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Crystal structure of a hydrogen sulfide-producing enzyme (FN1220) from fusobacterium nucleatum in complex with L-lanthionine-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
- 5XEM
- Type
- protein
- Length
- 603 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, 85F, CA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine synthase (EC 2.5.1.47) | protein | 302 | 43% 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 · 3 copies · chains A, B
- 85F · (2R)-2-azanyl-3-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 12 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.74 | 0.89 | 49 | 85F, PLP |
| 2 | 214 | 0.71 | 0.87 | 49 | PLP, 85F, ACT |
| 3 | 233 | 0.64 | 0.82 | 37 | empty |
| 4 | 63 | 0.57 | 0.89 | 25 | empty |
| 5 | 100 | 0.47 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1669 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5XEM · Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium… · 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 Q8RE94
- Elsewhere: RCSB PDB 5XEM · PDBe 5XEM · UniProt Q8RE94
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