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Structure of N-acylhomoserine lactone acylase macq in complex with decanoic acid

Analyse Structure of N-acylhomoserine lactone acylase macq in complex with decanoic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YFA
Type: protein
Length: 3,029 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein related to penicillin acylase
UniProt: A0A0A1VBK6
Ligands: DKA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J	Protein related to penicillin acylase	protein	167	59% helix, 8% strand	A0A0A1VBK6
B, H, K	Protein related to penicillin acylase	protein	16	19% helix, 0% strand	A0A0A1VBK6
C, F, I	Protein related to penicillin acylase	protein	574	27% helix, 30% strand	A0A0A1VBK6
D	Protein related to penicillin acylase	protein	168	61% helix, 8% strand	A0A0A1VBK6
E	Protein related to penicillin acylase	protein	15	20% helix, 0% strand	A0A0A1VBK6
L	Protein related to penicillin acylase	protein	575	27% helix, 30% strand	A0A0A1VBK6

Ligands and binding sites

DKA · Decanoic acid · ligand · 4 copies · chains A, C, F, G, I, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	948	0.79	0.81	115	empty
2	338	0.76	0.87	47	empty
3	71	0.75	0.98	22	DKA
4	70	0.74	0.97	21	DKA
5	70	0.73	0.97	21	DKA

Interfaces

30 interfaces between chains.

J–L · 4350 Å² buried · 76 hydrogen bonds · protein-protein
D–F · 4344 Å² buried · 86 hydrogen bonds · protein-protein
G–I · 4324 Å² buried · 84 hydrogen bonds · protein-protein
A–C · 4261 Å² buried · 75 hydrogen bonds · protein-protein
C–I · 681 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

4YFA · Structure of N-acylhomoserine lactone acylase MacQ in complex with decanoic acid · 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 A0A0A1VBK6
Elsewhere: RCSB PDB 4YFA · PDBe 4YFA · UniProt A0A0A1VBK6

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