MolNFT v1 · #119338 · protein
Crystal structure of the cysteine desulfurase csda from escherichia COLI at 1.996 angstroem resolution
5FT4: “Crystal structure of the cysteine desulfurase csda from escherichia COLI at 1.996 angstroem resolution”. X-ray diffraction, 1 ligand (PLP), 4 pockets (best druggability 0.81). MolNFT v1 #119338 on GenesisL1: 3D structure, binding…
- PDB
- 5FT4
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase csda
- EC
- 2.8.1.7, 4.4.1.-, 4.4.1.16
- UniProt
- Q46925
- Ligands
- PLP
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cysteine desulfurase csda (EC 2.8.1.7, 4.4.1.-, 4.4.1.16) | protein | 399 | 43% helix, 17% strand | Q46925 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- CIT · Citric acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.81 | 0.82 | 174 | PLP, GOL, CIT |
| 2 | 222 | 0.61 | 0.81 | 29 | GOL |
| 3 | 78 | 0.42 | 0.79 | 20 | empty |
| 4 | 84 | 0.41 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3315 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5FT4 · Crystal structure of the cysteine desulfurase CsdA from Escherichia coli at 1.996… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46925 · AlphaFold monomer V2.0 prediction for cysteine desulfurase csda (Q46925) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q46925
- Elsewhere: RCSB PDB 5FT4 · PDBe 5FT4 · UniProt Q46925
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