MolNFT v1 · #119341 · protein
Crystal structure of the complex between the cysteine desulfurase csda and the sulfur-acceptor csde in the persulfurated state at 2.50 angstroem resolution
5FT8: “Crystal structure of the complex between the cysteine desulfurase csda and the sulfur-acceptor csde in the…”. X-ray diffraction, 2 ligands (CSS, PLP), 20 pockets (best druggability 0.82). MolNFT v1 #119341 on GenesisL1: 3D…
- PDB
- 5FT8
- Type
- protein
- Length
- 4,281 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase csda; Sulfur acceptor protein csde
- EC
- 2.8.1.7, 4.4.1.-, 4.4.1.16
- UniProt
- Q46925, P0AGF2
- Ligands
- CSS, PLP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Cysteine desulfurase csda (EC 2.8.1.7, 4.4.1.-, 4.4.1.16) | protein | 400 | 44% helix, 18% strand | Q46925 |
| B | Sulfur acceptor protein csde | protein | 147 | 49% helix, 16% strand | P0AGF2 |
| D | Sulfur acceptor protein csde | protein | 143 | 50% helix, 17% strand | P0AGF2 |
| F | Sulfur acceptor protein csde | protein | 135 | 48% helix, 17% strand | P0AGF2 |
| H | Sulfur acceptor protein csde | protein | 144 | 46% helix, 18% strand | P0AGF2 |
| J | Sulfur acceptor protein csde | protein | 141 | 48% helix, 17% strand | P0AGF2 |
| L, N | Sulfur acceptor protein csde | protein | 139 | 47% helix, 17% strand | P0AGF2 |
| M, O | Cysteine desulfurase csda (EC 2.8.1.7, 4.4.1.-, 4.4.1.16) | protein | 398 | 44% helix, 18% strand | Q46925 |
| P | Sulfur acceptor protein csde | protein | 97 | 63% helix, 2% strand | P0AGF2 |
Ligands and binding sites
- CSS · S-mercaptocysteine · ligand · 15 copies · chains A, C, B, D, E, G, F, H, I, K, J, L, M, O, N
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, C, E, G, I, K, M, O
- GOL · Glycerol · additive · 51 copies · chains A, B, C, D, E, G, H, I, K, M
- PEG · Di(hydroxyethyl)ether · additive · 16 copies · chains A, C, B, E, G, H, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.82 | 0.83 | 103 | PLP, CSS, PEG |
| 2 | 852 | 0.80 | 0.83 | 88 | PLP, CSS |
| 3 | 1105 | 0.80 | 0.82 | 111 | PLP, CSS, GOL |
| 4 | 1053 | 0.79 | 0.81 | 99 | PLP, CSS |
| 5 | 1102 | 0.79 | 0.81 | 119 | PLP, CSS |
Interfaces
31 interfaces between chains.
- A–C · 3250 Ų buried · 37 hydrogen bonds · protein-protein
- E–G · 3221 Ų buried · 38 hydrogen bonds · protein-protein
- M–O · 3143 Ų buried · 37 hydrogen bonds · protein-protein
- I–K · 2995 Ų buried · 36 hydrogen bonds · protein-protein
- I–J · 812 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 covalent, 8 cofactor (covalent ligand, pyridoxal phosphate Schiff base).
Compared structures
- 5FT8 · Crystal structure of the complex between the cysteine desulfurase CsdA and the… · the same entry in another collection · chain C against C, TM-score 1.00
- Q46925 · AlphaFold monomer V2.0 prediction for cysteine desulfurase csda (Q46925) · a predicted model of the same protein · chain O 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 P0AGF2
- Elsewhere: RCSB PDB 5FT8 · PDBe 5FT8 · UniProt Q46925 · UniProt P0AGF2
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