MolNFT v1 · #111056 · protein

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

4YFB · Protein related to penicillin acylase: “Structure of N-acylhomoserine lactone acylase macq in complex with phenylacetic acid”. X-ray diffraction, 1 ligand (PAC), 20 pockets (best druggability 0.83). MolNFT v1 #111056 on GenesisL1…

PDB: 4YFB
Type: protein
Length: 3,033 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein related to penicillin acylase
UniProt: A0A0A1VBK6
Ligands: PAC
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Protein related to penicillin acylase	protein	168	60% helix, 9% strand	A0A0A1VBK6
B, H	Protein related to penicillin acylase	protein	15	20% helix, 0% strand	A0A0A1VBK6
C, F, I	Protein related to penicillin acylase	protein	575	28% helix, 30% strand	A0A0A1VBK6
E	Protein related to penicillin acylase	protein	14	21% helix, 0% strand	A0A0A1VBK6
G	Protein related to penicillin acylase	protein	171	60% helix, 9% strand	A0A0A1VBK6
J	Protein related to penicillin acylase	protein	167	60% helix, 8% strand	A0A0A1VBK6
K	Protein related to penicillin acylase	protein	16	19% helix, 0% strand	A0A0A1VBK6
L	Protein related to penicillin acylase	protein	574	27% helix, 30% strand	A0A0A1VBK6

Ligands and binding sites

PAC · 2-phenylacetic acid · ligand · 4 copies · chains C, F, I, L
GOL · Glycerol · additive · 4 copies · chains C, F, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1039	0.83	0.84	127	empty
2	1146	0.75	0.78	113	empty
3	69	0.75	0.98	22	PAC
4	70	0.74	0.98	21	PAC
5	60	0.72	0.98	16	PAC

Interfaces

28 interfaces between chains.

G–I · 4411 Å² buried · 84 hydrogen bonds · protein-protein
A–C · 4391 Å² buried · 83 hydrogen bonds · protein-protein
D–F · 4372 Å² buried · 88 hydrogen bonds · protein-protein
J–L · 4293 Å² buried · 85 hydrogen bonds · protein-protein
C–I · 789 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4YFB · Structure of N-acylhomoserine lactone acylase MacQ in complex with phenylacetic 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 4YFB · PDBe 4YFB · UniProt A0A0A1VBK6

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