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Crystal structure of the human mitochondrial cysteine desulfurase with active cysteine loop within ISCU1 active site, coordinating zn ion. complexed with human ISD11 and E. COLI ACP1 at 3.3A.

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

PDB: 5WLW
Type: protein
Length: 1,357 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, ZN
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	399	42% helix, 15% strand	Q9Y697
B	Lyr motif-containing protein 4	protein	81	72% helix, 1% strand	Q9HD34
C	Acyl carrier protein	protein	71	61% helix, 3% strand	B7MJ81
D	Iron-sulfur cluster assembly enzyme iscu, mitochondrial	protein	128	46% helix, 21% strand	Q9H1K1
E	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	401	41% helix, 16% strand	Q9Y697
F	Lyr motif-containing protein 4	protein	83	71% helix, 1% strand	Q9HD34
G	Acyl carrier protein	protein	70	53% helix, 3% strand	B7MJ81
H	Iron-sulfur cluster assembly enzyme iscu, mitochondrial	protein	124	44% helix, 22% 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
ZN · Zinc ion · metal · 2 copies · chains A, D, E, H

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

Pockets

16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	611	0.78	0.84	68	PLP
2	109	0.76	0.96	37	empty
3	578	0.75	0.82	59	PLP
4	536	0.73	0.81	51	8Q1
5	102	0.73	0.94	27	empty

Interfaces

11 interfaces between chains.

A–E · 2197 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 1116 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1043 Å² buried · 13 hydrogen bonds · protein-protein
E–H · 1006 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 945 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5WLW · Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine… · 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
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 0.98

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 5WLW · PDBe 5WLW · UniProt Q9Y697 · UniProt Q9HD34 · UniProt B7MJ81 · UniProt Q9H1K1

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