PDB-2hu8: Binding of inhibitors by Acylaminoacyl peptidase

ID or keywords:

Entry

Database: PDB / ID: 2hu8

Title

Binding of inhibitors by Acylaminoacyl peptidase

Components

Acylamino-acid-releasing enzyme

Keywords

HYDROLASE / alpha/beta hydrolase / beta-propeller / enzyme-inhibitor complex

Function / homology

Function and homology information

acylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function

Biological species

Aeropyrum pernix (archaea)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Kiss, A.L. / Hornung, B. / Radi, K. / Gengeliczki, Z. / Sztaray, B. / Harmat, V. / Polgar, L.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: The Acylaminoacyl Peptidase from Aeropyrum pernix K1 Thought to Be an Exopeptidase Displays Endopeptidase Activity
Authors: Kiss, A.L. / Hornung, B. / Radi, K. / Gengeliczki, Z. / Sztaray, B. / Juhasz, T. / Szeltner, Z. / Harmat, V. / Polgar, L.

History

Deposition	Jul 26, 2006	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 15, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Nov 10, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn / struct_ncs_dom_lim Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2hu8.cif.gz	218.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2hu8.ent.gz	171.7 KB	Display	PDB format
PDBx/mmJSON format	2hu8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2hu8_validation.pdf.gz	477.1 KB	Display	wwPDB validaton report
Full document	2hu8_full_validation.pdf.gz	484.3 KB	Display
Data in XML	2hu8_validation.xml.gz	46.3 KB	Display
Data in CIF	2hu8_validation.cif.gz	62.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hu/2hu8 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/2hu8	HTTPS FTP

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Related structure data

Related structure data	2hu5C 2hu7C C: citing same article (ref.)
Similar structure data	2hu5-d 2qr5-d 2hu7-d 1ve7-d 2qzp-d 1ve6-d 4re5-d 6z8e-d 6z8d-d 1lnw-5 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (2) #253 - Jan 2021 Expressome similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Acylamino-acid-releasing enzyme

B: Acylamino-acid-releasing enzyme

hetero molecules

127 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.810, 103.922, 169.255
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 2

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	GLY	GLY	A	A	24 - 29	24 - 29
2	1	1	LYS	LYS	GLY	GLY	B	B	24 - 29	24 - 29
3	2	1	VAL	VAL	VAL	VAL	A	A	31 - 39	31 - 39
4	2	1	VAL	VAL	VAL	VAL	B	B	31 - 39	31 - 39
5	3	1	ASN	ASN	TYR	TYR	A	A	47 - 51	47 - 51
6	3	1	ASN	ASN	TYR	TYR	B	B	47 - 51	47 - 51
7	4	1	VAL	VAL	ARG	ARG	A	A	57 - 61	57 - 61
8	4	1	VAL	VAL	ARG	ARG	B	B	57 - 61	57 - 61
9	5	1	PRO	PRO	HIS	HIS	A	A	63 - 71	63 - 71
10	5	1	PRO	PRO	HIS	HIS	B	B	63 - 71	63 - 71
11	6	1	GLY	GLY	THR	THR	A	A	73 - 130	73 - 130
12	6	1	GLY	GLY	THR	THR	B	B	73 - 130	73 - 130
13	7	1	VAL	VAL	ARG	ARG	A	A	134 - 145	134 - 145
14	7	1	VAL	VAL	ARG	ARG	B	B	134 - 145	134 - 145
15	8	1	LEU	LEU	GLY	GLY	A	A	147 - 161	147 - 161
16	8	1	LEU	LEU	GLY	GLY	B	B	147 - 161	147 - 161
17	9	1	LEU	LEU	SER	SER	A	A	163 - 180	163 - 180
18	9	1	LEU	LEU	SER	SER	B	B	163 - 180	163 - 180
19	10	1	SER	SER	PHE	PHE	A	A	184 - 190	184 - 190
20	10	1	SER	SER	PHE	PHE	B	B	184 - 190	184 - 190
21	11	1	GLY	GLY	THR	THR	A	A	193 - 214	193 - 214
22	11	1	GLY	GLY	THR	THR	B	B	193 - 214	193 - 214
23	12	1	ARG	ARG	SER	SER	A	A	219 - 229	219 - 229
24	12	1	ARG	ARG	SER	SER	B	B	219 - 229	219 - 229
25	13	1	PHE	PHE	TYR	TYR	A	A	240 - 243	240 - 243
26	13	1	PHE	PHE	TYR	TYR	B	B	240 - 243	240 - 243
27	14	1	ALA	ALA	PRO	PRO	A	A	247 - 255	247 - 255
28	14	1	ALA	ALA	PRO	PRO	B	B	247 - 255	247 - 255
29	15	1	GLY	GLY	VAL	VAL	A	A	257 - 278	257 - 278
30	15	1	GLY	GLY	VAL	VAL	B	B	257 - 278	257 - 278
31	16	1	PRO	PRO	LEU	LEU	A	A	281 - 302	281 - 302
32	16	1	PRO	PRO	LEU	LEU	B	B	281 - 302	281 - 302
33	17	1	THR	THR	GLY	GLY	A	A	304 - 320	304 - 320
34	17	1	THR	THR	GLY	GLY	B	B	304 - 320	304 - 320
1	1	2	SER	SER	VAL	VAL	A	A	10 - 13	10 - 13
2	1	2	SER	SER	VAL	VAL	B	B	10 - 13	10 - 13
3	2	2	ASP	ASP	VAL	VAL	A	A	15 - 22	15 - 22
4	2	2	ASP	ASP	VAL	VAL	B	B	15 - 22	15 - 22
5	3	2	PRO	PRO	SER	SER	A	A	323 - 344	323 - 344
6	3	2	PRO	PRO	SER	SER	B	B	323 - 344	323 - 344
7	4	2	VAL	VAL	PRO	PRO	A	A	346 - 359	346 - 359
8	4	2	VAL	VAL	PRO	PRO	B	B	346 - 359	346 - 359
9	5	2	THR	THR	THR	THR	A	A	362 - 380	362 - 380
10	5	2	THR	THR	THR	THR	B	B	362 - 380	362 - 380
11	6	2	ALA	ALA	VAL	VAL	A	A	382 - 472	382 - 472
12	6	2	ALA	ALA	VAL	VAL	B	B	382 - 472	382 - 472
13	7	2	TRP	TRP	SER	SER	A	A	474 - 496	474 - 496
14	7	2	TRP	TRP	SER	SER	B	B	474 - 496	474 - 496
15	8	2	ILE	ILE	MET	MET	A	A	499 - 500	499 - 500
16	8	2	ILE	ILE	MET	MET	B	B	499 - 500	499 - 500
17	9	2	SER	SER	PRO	PRO	A	A	502 - 505	502 - 505
18	9	2	SER	SER	PRO	PRO	B	B	502 - 505	502 - 505
19	10	2	ASN	ASN	ARG	ARG	A	A	507 - 581	507 - 581
20	10	2	ASN	ASN	ARG	ARG	B	B	507 - 581	507 - 581

NCS ensembles :

ID
1
2

Details

The biological assembly is the dimer in the asymmetric unit.

#1: Protein	Acylamino-acid-releasing enzyme / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase Mass: 63092.551 Da / Num. of mol.: 2 / Mutation: S445A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: Chemical	ChemComp-BE2 / 2-AMINOBENZOIC ACID Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₇NO₂
#3: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#4: Chemical	ChemComp-PHE / PHENYLALANINE Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₁NO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20mM Tris/HCl, 20% ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 21, 2005
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.4→19.96 Å / Num. obs: 45009 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / R_merge(I) obs: 0.137 / Net I/σ(I): 11.68
Reflection shell	Resolution: 2.4→2.5 Å / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 4.46 / Num. unique all: 5151 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→19.96 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.867 / SU B: 11.651 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.578 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26128	2264	5 %	RANDOM (as for related pdb entry 2HU5)
R_work	0.2155	-	-	-
all	0.21778	42954	-	-
obs	0.21778	42954	99.56 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 5.952 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	0 Å²	0 Å²
2-	-	-0.17 Å²	0 Å²
3-	-	-	0.42 Å²

Refine analyze

Luzzati coordinate error obs: 0.394 Å

Refinement step

Cycle: LAST / Resolution: 2.4→19.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8584	0	50	223	8857

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.021	8861
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8217
X-RAY DIFFRACTION	r_angle_refined_deg	0.878	1.97	12043
X-RAY DIFFRACTION	r_angle_other_deg	0.887	3	18951
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.791	5	1162
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1349
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	10081
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1865
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.3	1532
X-RAY DIFFRACTION	r_nbd_other	0.242	0.3	9111
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.5	5238
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.195	0.5	419
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.256	0.3	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.231	0.3	70
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.251	0.5	9
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.061	1.5	5708
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.109	2	9120
X-RAY DIFFRACTION	r_scbond_it	0.264	3	3153
X-RAY DIFFRACTION	r_scangle_it	0.414	4.5	2916
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	1449	tight positional	0.02	0.05
2	1523	tight positional	0.03	0.05
1	2103	medium positional	0.28	0.5
2	2260	medium positional	0.33	0.5
1	1449	tight thermal	0.02	0.5
2	1523	tight thermal	0.03	0.5
1	2103	medium thermal	0.1	2
2	2260	medium thermal	0.12	2

LS refinement shell

Resolution: 2.4→2.461 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.347	153
R_work	0.282	3075

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.8911	0.078	0.2444	1.0674	0.082	1.6782	-0.0609	-0.0287	0.1812	-0.0335	-0.0118	-0.0644	-0.2091	0.0075	0.0727	0.1351	-0.0029	-0.0537	0.072	-0.0028	0.1154	6.0867	40.475	19.5147
2	1.2305	-0.2341	0.6204	1.748	-0.0551	1.3155	0.014	-0.004	-0.0811	-0.0204	-0.049	-0.0905	0.0982	-0.017	0.035	0.054	0.0002	-0.039	0.0668	0.0138	0.0315	-1.6642	13.5795	17.3314
3	3.3666	-0.0347	0.8826	1.9641	-0.2732	0.9913	0.4701	0.5977	-0.6561	-0.4409	-0.1321	-0.2024	0.4002	0.2563	-0.3381	0.4891	0.0939	-0.1883	0.2344	-0.0912	0.4537	21.1905	-31.1245	22.4056
4	3.3399	-0.9675	1.3173	2.9473	-0.3834	0.9328	0.0643	0.3858	0.2641	-0.0715	-0.1729	-0.4809	0.0526	0.1654	0.1087	0.1085	-0.0015	-0.0467	0.174	0.0855	0.149	25.0555	-4.7313	30.3335

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	23 - 321	23 - 321
2	X-RAY DIFFRACTION	2	A	A	322 - 582	322 - 582
3	X-RAY DIFFRACTION	2	A	A	8 - 22	8 - 22
4	X-RAY DIFFRACTION	3	B	B	23 - 321	23 - 321
5	X-RAY DIFFRACTION	4	B	B	322 - 581	322 - 581
6	X-RAY DIFFRACTION	4	B	B	9 - 22	9 - 22

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