Structure of human mitochondrial complex NFS1-ISCU2 (wt)-ISD11 with E.COLI ACP1 at 1.8 a resolution (NIAU)2

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).

Ligands and binding sites

• PLP · Pyridoxal-5'-phosphate · ligand · chains A
• P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains A, D
• EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · chains B
• 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains A, B, C
• EDO · 1,2-ethanediol · additive · 48 copies · chains A, D, B, C
• PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, D, C
• GOL · Glycerol · additive · 6 copies · chains A, B, D
• PGE · Triethylene glycol · additive · 3 copies · chains A
• PG4 · Tetraethylene glycol · additive · 2 copies · chains A
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B, C
• 1PE · Pentaethylene glycol · additive · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1108 Ų buried · 14 hydrogen bonds · protein-protein
• A–D · 1097 Ų buried · 16 hydrogen bonds · protein-protein
• B–C · 549 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor, 1 covalent (pyridoxal phosphate Schiff base, covalent ligand).

Compared structures

• 6W1D · Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A… · the same entry in another collection · chain D against D, TM-score 1.00
• Q9Y697 · AlphaFold monomer V2.0 prediction for cysteine desulfurase, mitochondrial (Q9Y697) · a predicted model of the same protein · chain A against A, TM-score 1.00
• Q9H1K1 · AlphaFold monomer V2.0 prediction for iron-sulfur cluster assembly enzyme iscu… · a predicted model of the same protein · chain D against A, TM-score 0.98
• Q9HD34 · AlphaFold monomer V2.0 prediction for lyr motif-containing protein 4 (Q9HD34) · a predicted model of the same protein · chain B against A, TM-score 0.97
• B7MJ81 · AlphaFold monomer V2.0 prediction for acyl carrier protein (B7MJ81) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q9Y697
• Every structure of UniProt Q9HD34
• Every structure of UniProt B7MJ81
• Every structure of UniProt Q9H1K1
• Elsewhere: RCSB PDB 6W1D · PDBe 6W1D · UniProt Q9Y697 · UniProt Q9HD34 · UniProt B7MJ81 · UniProt Q9H1K1