MolNFT v1 · #103654 · protein

Crystal structure of 3-hydroxyacyl-CoA-dehydrogenase from brucella melitensis

4PN3 · 3-hydroxyacyl-CoA dehydrogenase: “Crystal structure of 3-hydroxyacyl-CoA-dehydrogenase from brucella melitensis”. X-ray diffraction, 16 pockets (best druggability 0.85). MolNFT v1 #103654 on GenesisL1: 3D structure, binding sites…

PDB: 4PN3
Type: protein
Length: 2,043 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-hydroxyacyl-CoA dehydrogenase
UniProt: N7K0F6
Pockets: 16 · best druggability 0.85

Structure

x-ray diffraction · 7 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3-hydroxyacyl-CoA dehydrogenase	protein	260	47% helix, 17% strand	N7K0F6
C	3-hydroxyacyl-CoA dehydrogenase	protein	259	47% helix, 17% strand	N7K0F6
D	3-hydroxyacyl-CoA dehydrogenase	protein	249	43% helix, 17% strand	N7K0F6
E	3-hydroxyacyl-CoA dehydrogenase	protein	257	47% helix, 18% strand	N7K0F6
F	3-hydroxyacyl-CoA dehydrogenase	protein	254	46% helix, 17% strand	N7K0F6
G	3-hydroxyacyl-CoA dehydrogenase	protein	256	48% helix, 17% strand	N7K0F6
H	3-hydroxyacyl-CoA dehydrogenase	protein	248	45% helix, 18% strand	N7K0F6

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D, E, F, G, 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1140	0.85	0.86	69	TRS
2	1143	0.84	0.85	69	TRS
3	972	0.83	0.84	125	empty
4	576	0.71	0.79	66	empty
5	477	0.68	0.79	64	empty

Interfaces

19 interfaces between chains.

B–C · 1892 Å² buried · 20 hydrogen bonds · protein-protein
F–G · 1878 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1851 Å² buried · 19 hydrogen bonds · protein-protein
E–H · 1848 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1748 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

4PN3 · Crystal structure of 3-hydroxyacyl-CoA-dehydrogenase from Brucella melitensis · the same entry in another collection · chain A against A, 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 N7K0F6
Elsewhere: RCSB PDB 4PN3 · PDBe 4PN3 · UniProt N7K0F6

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