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Crystal structure of human NFS1-ISD11 in complex with E. COLI acyl- carrier protein at 3.09 ångströms

Analyse Crystal structure of human NFS1-ISD11 in complex with E. COLI acyl- carrier… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5USR
Type: protein
Length: 1,952 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cysteine desulfurase, mitochondrial; Lyr motif-containing protein 4; Acyl carrier protein
EC: 2.8.1.7
UniProt: Q9Y697, Q9HD34, P0A6A8
Ligands: 8Q1
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 12 distinct chains · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	364	44% helix, 15% strand	Q9Y697
B	Lyr motif-containing protein 4	protein	76	79% helix, 0% strand	Q9HD34
C	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	352	44% helix, 15% strand	Q9Y697
D	Lyr motif-containing protein 4	protein	80	79% helix, 1% strand	Q9HD34
E	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	321	42% helix, 17% strand	Q9Y697
F	Lyr motif-containing protein 4	protein	75	84% helix, 0% strand	Q9HD34
G	Cysteine desulfurase, mitochondrial (EC 2.8.1.7)	protein	316	43% helix, 17% strand	Q9Y697
H	Lyr motif-containing protein 4	protein	77	78% helix, 0% strand	Q9HD34
I	Acyl carrier protein	protein	76	55% helix, 3% strand	P0A6A8
J	Acyl carrier protein	protein	75	57% helix, 3% strand	P0A6A8
K	Acyl carrier protein	protein	69	48% helix, 0% strand	P0A6A8
L	Acyl carrier protein	protein	71	48% helix, 0% strand	P0A6A8

Ligands and binding sites

8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 4 copies · chains E, F, I, G, H, J, A, B, K, C, D, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.82	0.83	110	empty
2	1062	0.80	0.81	89	empty
3	1196	0.78	0.80	110	empty
4	564	0.75	0.82	60	8Q1
5	332	0.74	0.85	38	8Q1

Interfaces

20 interfaces between chains.

E–F · 929 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 914 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 814 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 774 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 757 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 modified (covalent ligand, cofactor).

Compared structures

5USR · Crystal structure of human NFS1-ISD11 in complex with E. coli acyl-carrier protein at… · the same entry in another collection · chain L against L, TM-score 1.00

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 P0A6A8
Elsewhere: RCSB PDB 5USR · PDBe 5USR · UniProt Q9Y697 · UniProt Q9HD34 · UniProt P0A6A8

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