MolNFT v1 · #139402 · protein
Crystal structure of a hydrogen sulfide-producing enzyme (FN1220) from fusobacterium nucleatum
5XEO · Cysteine synthase: “Crystal structure of a hydrogen sulfide-producing enzyme (FN1220) from fusobacterium nucleatum”. X-ray diffraction, 2 ligands (PLP, CA), 6 pockets (best druggability 0.71). MolNFT v1 #139402 on GenesisL1: 3D…
- PDB
- 5XEO
- 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, CA
- Pockets
- 6 · best druggability 0.71
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 | 42% helix, 19% strand | Q8RE94 |
| B | Cysteine synthase (EC 2.5.1.47) | protein | 299 | 44% helix, 18% strand | Q8RE94 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 3 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.71 | 0.81 | 57 | PLP |
| 2 | 356 | 0.70 | 0.83 | 53 | empty |
| 3 | 194 | 0.68 | 0.87 | 46 | PLP, ACT |
| 4 | 97 | 0.58 | 0.86 | 25 | empty |
| 5 | 62 | 0.32 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5XEO · 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 5XEO · PDBe 5XEO · UniProt Q8RE94
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