MolNFT v1 · #99190 · protein
Structural changes during cysteine desulfurase csda and sulfur- acceptor csde interactions provide insight into the trans- persulfuration
4LW4 · Cysteine sulfinate desulfinase: “Structural changes during cysteine desulfurase csda and sulfur- acceptor csde interactions provide insight…”. X-ray diffraction, 1 ligand (PLP), 6 pockets (best druggability 0.84). MolNFT v1 #99190…
- PDB
- 4LW4
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine sulfinate desulfinase; Cysteine desulfuration protein csde
- EC
- 4.4.1.-
- UniProt
- Q46925, D5CZ88
- Ligands
- PLP
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine sulfinate desulfinase (EC 4.4.1.-) | protein | 392 | 43% helix, 18% strand | Q46925 |
| B | Cysteine sulfinate desulfinase (EC 4.4.1.-) | protein | 398 | 45% helix, 17% strand | Q46925 |
| C | Cysteine desulfuration protein csde | protein | 145 | 48% helix, 12% strand | D5CZ88 |
| D | Cysteine desulfuration protein csde | protein | 137 | 51% helix, 15% strand | D5CZ88 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 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 | 1145 | 0.84 | 0.85 | 115 | PLP |
| 2 | 949 | 0.80 | 0.82 | 101 | PLP |
| 3 | 231 | 0.61 | 0.80 | 37 | empty |
| 4 | 59 | 0.49 | 0.85 | 17 | empty |
| 5 | 59 | 0.35 | 0.77 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2899 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 800 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 683 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 97 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4LW4 · Structural changes during cysteine desulfurase CsdA and sulfur-acceptor CsdE interactions… · 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 A 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
- Every structure of UniProt D5CZ88
- Elsewhere: RCSB PDB 4LW4 · PDBe 4LW4 · UniProt Q46925 · UniProt D5CZ88
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