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Crystal structure of a putative 3-ketoacyl-(acyl-carrier-protein) reductase from mycobacterium paratuberculosis in complex with NAD

Analyse Crystal structure of a putative 3-ketoacyl-(acyl-carrier-protein) reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SX2
Type: protein
Length: 2,097 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
UniProt: Q73W00
Ligands: NAD
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 7 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative 3-ketoacyl-(acyl-carrier-protein) reductase	protein	268	47% helix, 15% strand	Q73W00
B, C	Putative 3-ketoacyl-(acyl-carrier-protein) reductase	protein	257	48% helix, 16% strand	Q73W00
D	Putative 3-ketoacyl-(acyl-carrier-protein) reductase	protein	269	49% helix, 15% strand	Q73W00
E	Putative 3-ketoacyl-(acyl-carrier-protein) reductase	protein	256	48% helix, 16% strand	Q73W00
F	Putative 3-ketoacyl-(acyl-carrier-protein) reductase	protein	274	48% helix, 15% strand	Q73W00
G	Putative 3-ketoacyl-(acyl-carrier-protein) reductase	protein	267	48% helix, 15% strand	Q73W00
H	Putative 3-ketoacyl-(acyl-carrier-protein) reductase	protein	249	48% helix, 16% strand	Q73W00

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, D, E, H, F, G

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	652	0.86	0.90	66	NAD
2	663	0.85	0.89	66	NAD
3	440	0.85	0.92	59	NAD, MPD
4	464	0.85	0.91	62	NAD, MPD
5	876	0.84	0.86	92	empty

Interfaces

13 interfaces between chains.

F–G · 1497 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1488 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1487 Å² buried · 16 hydrogen bonds · protein-protein
E–H · 1279 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1196 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3SX2 · Crystal structure of a putative 3-ketoacyl-(acyl-carrier-protein) reductase from… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt Q73W00
Elsewhere: RCSB PDB 3SX2 · PDBe 3SX2 · UniProt Q73W00

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