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Structure of FADD32 from mycobacterium smegmatis complexed to AMPC20

Analyse Structure of FADD32 from mycobacterium smegmatis complexed to AMPC20 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EY8
Type: protein
Length: 4,790 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-CoA synthase
UniProt: A0R618
Ligands: 5SV
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 31% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acyl-CoA synthase	protein	598	32% helix, 24% strand	A0R618
B	Acyl-CoA synthase	protein	594	31% helix, 24% strand	A0R618
C	Acyl-CoA synthase	protein	605	31% helix, 25% strand	A0R618
D	Acyl-CoA synthase	protein	603	32% helix, 25% strand	A0R618
E	Acyl-CoA synthase	protein	592	32% helix, 23% strand	A0R618
F	Acyl-CoA synthase	protein	606	31% helix, 25% strand	A0R618
G	Acyl-CoA synthase	protein	597	32% helix, 25% strand	A0R618
H	Acyl-CoA synthase	protein	595	31% helix, 23% strand	A0R618

Ligands and binding sites

5SV · [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
GOL · Glycerol · additive · 2 copies · chains E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	975	0.87	0.88	113	5SV
2	1083	0.86	0.87	106	5SV
3	1084	0.86	0.86	130	5SV
4	1129	0.85	0.86	115	5SV, GOL
5	1143	0.85	0.86	113	5SV, GOL

Interfaces

12 interfaces between chains.

A–D · 563 Å² buried · 3 hydrogen bonds · protein-protein
F–H · 522 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 478 Å² buried · 8 hydrogen bonds · protein-protein
E–G · 453 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 423 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5EY8 · Structure of FadD32 from Mycobacterium smegmatis complexed to AMPC20 · the same entry in another collection · chain C against C, TM-score 1.00
A0R618 · AlphaFold monomer V2.0 prediction for long-chain-fatty-acid--AMP ligase FADD32 (A0R618) · a predicted model of the same protein · chain C 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 A0R618
Elsewhere: RCSB PDB 5EY8 · PDBe 5EY8 · UniProt A0R618

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