MolNFT v1 · #141373 · protein
Crystal structure of hydrogen sulfide-producing enzyme (FN1055) from fusobacterium nucleatum: lysine-dimethylated form
5Z5C · Cysteine synthase: “Crystal structure of hydrogen sulfide-producing enzyme (FN1055) from fusobacterium nucleatum…”. X-ray diffraction, 2 ligands (PLP, CL), 20 pockets (best druggability 0.76). MolNFT v1 #141373 on GenesisL1: 3D…
- PDB
- 5Z5C
- Type
- protein
- Length
- 1,331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine synthase
- EC
- 2.5.1.47
- UniProt
- Q8REP3
- Ligands
- PLP, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine synthase (EC 2.5.1.47) | protein | 331 | 40% helix, 20% strand | Q8REP3 |
| B | Cysteine synthase (EC 2.5.1.47) | protein | 336 | 41% helix, 21% strand | Q8REP3 |
| C, D | Cysteine synthase (EC 2.5.1.47) | protein | 332 | 40% helix, 20% strand | Q8REP3 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.76 | 0.84 | 69 | PLP |
| 2 | 61 | 0.72 | 0.98 | 23 | PLP |
| 3 | 57 | 0.72 | 0.98 | 28 | PLP |
| 4 | 54 | 0.71 | 0.99 | 24 | PLP |
| 5 | 373 | 0.62 | 0.78 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1800 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1793 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 316 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 143 modified, 4 cofactor (methylation, pyridoxal phosphate Schiff base).
Compared structures
- 5Z5C · Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) 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 Q8REP3
- Elsewhere: RCSB PDB 5Z5C · PDBe 5Z5C · UniProt Q8REP3
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