PDB-2hu5: Binding of inhibitors by Acylaminoacyl-peptidase

ID or keywords:

Entry

Database: PDB / ID: 2hu5

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 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	Oct 25, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2hu5.cif.gz	230.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2hu5.ent.gz	182.9 KB	Display	PDB format
PDBx/mmJSON format	2hu5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2hu5_validation.pdf.gz	474.7 KB	Display	wwPDB validaton report
Full document	2hu5_full_validation.pdf.gz	482.6 KB	Display
Data in XML	2hu5_validation.xml.gz	42.8 KB	Display
Data in CIF	2hu5_validation.cif.gz	61.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hu/2hu5 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/2hu5	HTTPS FTP

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Related structure data

Related structure data	2hu7C 2hu8C 1ve6S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2hu7-d 2hu8-d 2qr5-d 1ve7-d 1ve6-d 2qzp-d 4re5-d 6z8d-d 6z8e-d 6z8f-d 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)	63.400, 103.334, 168.224
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:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-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	SER	SER	ILE	ILE	A	A	10 - 12	10 - 12
2	1	SER	SER	ILE	ILE	B	B	10 - 12	10 - 12
3	2	ASP	ASP	GLU	GLU	A	A	15 - 17	15 - 17
4	2	ASP	ASP	GLU	GLU	B	B	15 - 17	15 - 17
5	3	LEU	LEU	ALA	ALA	A	A	19 - 21	19 - 21
6	3	LEU	LEU	ALA	ALA	B	B	19 - 21	19 - 21
7	4	GLU	GLU	LEU	LEU	A	A	23 - 37	23 - 37
8	4	GLU	GLU	LEU	LEU	B	B	23 - 37	23 - 37
9	5	VAL	VAL	TYR	TYR	A	A	39 - 51	39 - 51
10	5	VAL	VAL	TYR	TYR	B	B	39 - 51	39 - 51
11	6	GLY	GLY	PRO	PRO	A	A	53 - 70	53 - 70
12	6	GLY	GLY	PRO	PRO	B	B	53 - 70	53 - 70
13	7	GLY	GLY	SER	SER	A	A	73 - 98	73 - 98
14	7	GLY	GLY	SER	SER	B	B	73 - 98	73 - 98
15	8	PRO	PRO	GLY	GLY	A	A	100 - 121	100 - 121
16	8	PRO	PRO	GLY	GLY	B	B	100 - 121	100 - 121
17	9	ALA	ALA	THR	THR	A	A	123 - 130	123 - 130
18	9	ALA	ALA	THR	THR	B	B	123 - 130	123 - 130
19	10	VAL	VAL	ALA	ALA	A	A	134 - 148	134 - 148
20	10	VAL	VAL	ALA	ALA	B	B	134 - 148	134 - 148
21	11	LEU	LEU	GLY	GLY	A	A	150 - 161	150 - 161
22	11	LEU	LEU	GLY	GLY	B	B	150 - 161	150 - 161
23	12	LEU	LEU	SER	SER	A	A	163 - 180	163 - 180
24	12	LEU	LEU	SER	SER	B	B	163 - 180	163 - 180
25	13	SER	SER	PHE	PHE	A	A	184 - 190	184 - 190
26	13	SER	SER	PHE	PHE	B	B	184 - 190	184 - 190
27	14	SER	SER	PHE	PHE	A	A	192 - 197	192 - 197
28	14	SER	SER	PHE	PHE	B	B	192 - 197	192 - 197
29	15	ALA	ALA	THR	THR	A	A	200 - 214	200 - 214
30	15	ALA	ALA	THR	THR	B	B	200 - 214	200 - 214
31	16	ALA	ALA	PHE	PHE	A	A	218 - 240	218 - 240
32	16	ALA	ALA	PHE	PHE	B	B	218 - 240	218 - 240
33	17	TYR	TYR	TRP	TRP	A	A	243 - 291	243 - 291
34	17	TYR	TYR	TRP	TRP	B	B	243 - 291	243 - 291
35	18	LEU	LEU	LEU	LEU	A	A	295 - 318	295 - 318
36	18	LEU	LEU	LEU	LEU	B	B	295 - 318	295 - 318
37	19	ARG	ARG	ALA	ALA	A	A	327 - 331	327 - 331
38	19	ARG	ARG	ALA	ALA	B	B	327 - 331	327 - 331
39	20	LEU	LEU	VAL	VAL	A	A	335 - 338	335 - 338
40	20	LEU	LEU	VAL	VAL	B	B	335 - 338	335 - 338
41	21	SER	SER	VAL	VAL	A	A	340 - 350	340 - 350
42	21	SER	SER	VAL	VAL	B	B	340 - 350	340 - 350
43	22	SER	SER	ALA	ALA	A	A	353 - 427	353 - 427
44	22	SER	SER	ALA	ALA	B	B	353 - 427	353 - 427
45	23	GLU	GLU	TYR	TYR	A	A	432 - 478	432 - 478
46	23	GLU	GLU	TYR	TYR	B	B	432 - 478	432 - 478
47	24	LEU	LEU	SER	SER	A	A	480 - 496	480 - 496
48	24	LEU	LEU	SER	SER	B	B	480 - 496	480 - 496
49	25	ILE	ILE	MET	MET	A	A	499 - 500	499 - 500
50	25	ILE	ILE	MET	MET	B	B	499 - 500	499 - 500
51	26	SER	SER	PRO	PRO	A	A	502 - 505	502 - 505
52	26	SER	SER	PRO	PRO	B	B	502 - 505	502 - 505
53	27	ASN	ASN	ASP	ASP	A	A	507 - 510	507 - 510
54	27	ASN	ASN	ASP	ASP	B	B	507 - 510	507 - 510
55	28	ILE	ILE	PHE	PHE	A	A	512 - 546	512 - 546
56	28	ILE	ILE	PHE	PHE	B	B	512 - 546	512 - 546
57	29	ALA	ALA	THR	THR	A	A	548 - 560	548 - 560
58	29	ALA	ALA	THR	THR	B	B	548 - 560	548 - 560
59	30	GLU	GLU	LYS	LYS	A	A	562 - 566	562 - 566
60	30	GLU	GLU	LYS	LYS	B	B	562 - 566	562 - 566
61	31	LEU	LEU	GLU	GLU	A	A	568 - 580	568 - 580
62	31	LEU	LEU	GLU	GLU	B	B	568 - 580	568 - 580

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: 63108.551 Da / Num. of mol.: 2 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-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#3: Chemical	ChemComp-PHE / PHENYLALANINE Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₁NO₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.18 Å³/Da / Density % sol: 43.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 78mM sodium acetate, 0.44mM EDTA, 2.2%PEG 4000, 0.56% beta-octyl-glucoside, 10% DMSO, pH 5.0, 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: May 18, 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→19.726 Å / Num. obs: 67288 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / R_merge(I) obs: 0.098 / Net I/σ(I): 15.12
Reflection shell	Resolution: 2→2.1 Å / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5399 / % possible all: 53.3

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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
Starting model: PDB ENTRY 1VE6

1ve6

Resolution: 2→19.726 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.916 / SU B: 5.208 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic and TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22441	3377	5 %	RANDOM
R_work	0.18147	-	-	-
all	0.18363	63906	-	-
obs	0.18363	63906	89.26 %	-

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: 17.716 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0 Å²	0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	-0.06 Å²

Refine analyze

Luzzati coordinate error obs: 0.269 Å

Refinement step

Cycle: LAST / Resolution: 2→19.726 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8658	0	62	332	9052

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	8935
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	8304
X-RAY DIFFRACTION	r_angle_refined_deg	1.308	1.972	12115
X-RAY DIFFRACTION	r_angle_other_deg	0.762	3	19194
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.469	5	1160
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	0.071	0.2	1345
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10111
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1883
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	1926
X-RAY DIFFRACTION	r_nbd_other	0.248	0.2	10742
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	6095
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	495
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	0.231	0.2	25
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.259	0.2	95
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.2	0.2	14
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	0.472	1.5	5704
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.88	2	9121
X-RAY DIFFRACTION	r_scbond_it	1.551	3	3231
X-RAY DIFFRACTION	r_scangle_it	2.617	4.5	2988
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 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
2988	medium positional	0.15	0.5
4415	loose positional	0.34	5
2988	medium thermal	0.59	2
4415	loose thermal	1.01	10

LS refinement shell

Resolution: 2→2.051 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.332	115
R_work	0.299	2554

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	0.4381	0.138	0.1611	1.0437	0.1521	0.5733	0.0103	0.0185	0.0045	-0.0534	0.0006	-0.0263	-0.0595	0.0007	-0.0109	0.0235	0.0182	-0.0196	0.0556	0.0024	0.0237	2.732	27.5864	18.2487
2	0.9283	0.1418	0.2693	1.608	-0.0039	0.4527	-0.0065	0.1397	-0.0695	-0.2229	0.027	-0.0831	0.0723	0.055	-0.0205	0.0661	-0.0089	-0.0311	0.0958	0.0158	0.0522	22.7987	-17.795	26.414

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	9 - 581	9 - 581
2	X-RAY DIFFRACTION	2	B	B	8 - 582	8 - 582

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