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Crystal structure of the human mitochondrial cysteine desulfurase in complex with ISD11 and iron-sulfur cluster scaffold protein ISCU1, and E. COLI ACP1 protein at 3.15A

Analyse Crystal structure of the human mitochondrial cysteine desulfurase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WKP
Type: protein
Length: 1,344 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cysteine desulfurase, mitochondrial; Lyr motif-containing protein 4; Acyl carrier…
EC: 2.8.1.7
UniProt: Q9Y697, Q9HD34, B7MJ81, Q9H1K1
Ligands: PLP, 8Q1
Pockets: 15 · best druggability 0.77

Structure

x-ray diffraction · 8 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	396	42% helix, 15% strand	Q9Y697
B	Lyr motif-containing protein 4	protein	81	77% helix, 1% strand	Q9HD34
C	Acyl carrier protein	protein	72	54% helix, 3% strand	B7MJ81
D	Iron-sulfur cluster assembly enzyme iscu, mitochondrial	protein	118	39% helix, 23% strand	Q9H1K1
E	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	398	41% helix, 15% strand	Q9Y697
F	Lyr motif-containing protein 4	protein	82	76% helix, 1% strand	Q9HD34
G	Acyl carrier protein	protein	71	54% helix, 3% strand	B7MJ81
H	Iron-sulfur cluster assembly enzyme iscu, mitochondrial	protein	126	43% helix, 21% strand	Q9H1K1

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, E
8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains A, B, C, E, F, G

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	962	0.77	0.80	100	PLP
2	836	0.76	0.80	111	PLP
3	535	0.74	0.82	52	8Q1
4	490	0.72	0.81	51	8Q1
5	68	0.70	0.96	20	empty

Interfaces

11 interfaces between chains.

A–E · 2152 Å² buried · 28 hydrogen bonds · protein-protein
E–H · 1147 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1144 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1097 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 836 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor, 2 covalent (pyridoxal phosphate Schiff base, covalent ligand).

Compared structures

5WKP · Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11… · the same entry in another collection · chain H against H, 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 0.99
Q9H1K1 · AlphaFold monomer V2.0 prediction for iron-sulfur cluster assembly enzyme iscu… · a predicted model of the same protein · chain H against A, TM-score 0.99
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 0.99

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 Q9Y697
Every structure of UniProt Q9HD34
Every structure of UniProt B7MJ81
Every structure of UniProt Q9H1K1
Elsewhere: RCSB PDB 5WKP · PDBe 5WKP · UniProt Q9Y697 · UniProt Q9HD34 · UniProt B7MJ81 · UniProt Q9H1K1

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