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- PDB-2hu7: Binding of inhibitors by Acylaminoacyl peptidase -

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Basic information

Entry
Database: PDB / ID: 2hu7
TitleBinding of inhibitors by Acylaminoacyl peptidase
ComponentsAcylamino-acid-releasing enzyme
KeywordsHYDROLASE / 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
Peptidase/esterase 'gauge' domain / : / Acylamino-acid-releasing enzyme-like, N-terminal domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Peptidase/esterase 'gauge' domain / : / Acylamino-acid-releasing enzyme-like, N-terminal domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / PHENYLALANINE / Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKiss, 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.
#1: Journal: Structure / Year: 2004
Title: Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1
Authors: Bartlam, M. / Wang, G. / Yang, H. / Gao, R. / Zhao, X. / Xie, G. / Cao, S. / Feng, Y. / Rao, Z.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8208
Polymers126,2172
Non-polymers6036
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-23 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.682, 103.989, 168.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
371A
381B
391A
401B
411A
421B
431A
441B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVALAA22 - 3022 - 30
21VALVALVALVALBB22 - 3022 - 30
32ASNASNASPASPAA47 - 5247 - 52
42ASNASNASPASPBB47 - 5247 - 52
53VALVALTYRTYRAA57 - 7257 - 72
63VALVALTYRTYRBB57 - 7257 - 72
74VALVALASPASPAA77 - 8277 - 82
84VALVALASPASPBB77 - 8277 - 82
95HISHISPROPROAA90 - 10090 - 100
105HISHISPROPROBB90 - 10090 - 100
116LEULEUGLYGLYAA106 - 161106 - 161
126LEULEUGLYGLYBB106 - 161106 - 161
137ALAALATHRTHRAA165 - 179165 - 179
147ALAALATHRTHRBB165 - 179165 - 179
158GLYGLYSERSERAA186 - 198186 - 198
168GLYGLYSERSERBB186 - 198186 - 198
179VALVALASPASPAA261 - 274261 - 274
189VALVALASPASPBB261 - 274261 - 274
1910GLUGLULEULEUAA279 - 290279 - 290
2010GLUGLULEULEUBB279 - 290279 - 290
2111VALVALTHRTHRAA296 - 300296 - 300
2211VALVALTHRTHRBB296 - 300296 - 300
2312ARGARGVALVALAA345 - 350345 - 350
2412ARGARGVALVALBB345 - 350345 - 350
2513THRTHRALAALAAA362 - 382362 - 382
2613THRTHRALAALABB362 - 382362 - 382
2714LEULEUALAALAAA385 - 425385 - 425
2814LEULEUALAALABB385 - 425385 - 425
2915ARGARGLEULEUAA431 - 435431 - 435
3015ARGARGLEULEUBB431 - 435431 - 435
3116ALAALAGLYGLYAA436 - 468436 - 468
3216ALAALAGLYGLYBB436 - 468436 - 468
3317SERSERTHRTHRAA481 - 493481 - 493
3417SERSERTHRTHRBB481 - 493481 - 493
3518ARGARGGLUGLUAA503 - 514503 - 514
3618ARGARGGLUGLUBB503 - 514503 - 514
3719LEULEUILEILEAA516 - 519516 - 519
3819LEULEUILEILEBB516 - 519516 - 519
3920GLUGLUGLYGLYAA538 - 543538 - 543
4020GLUGLUGLYGLYBB538 - 543538 - 543
4121ILEILETHRTHRAA550 - 560550 - 560
4221ILEILETHRTHRBB550 - 560550 - 560
4322LEULEUARGARGAA568 - 579568 - 579
4422LEULEUARGARGBB568 - 579568 - 579
DetailsThe biological assembly is the dimer in the asymmetric unit.

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Components

#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-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 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, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 3, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.537 Å / Num. obs: 76464 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.115 / Net I/σ(I): 13.07
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.1 / Num. unique all: 8216 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VE6

1ve6


Resolution: 2.01→19.52 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.633 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC AND TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21693 3602 5 %RANDOM (AS FOR RELATED PDB ENTRY 2HU5)
Rwork0.17554 ---
all0.17761 68079 --
obs0.17761 68079 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.241 Å
Refinement stepCycle: LAST / Resolution: 2.01→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8623 0 42 349 9014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0218890
X-RAY DIFFRACTIONr_bond_other_d0.0020.028241
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.97112067
X-RAY DIFFRACTIONr_angle_other_deg0.838319034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42151152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.21343
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210074
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021869
X-RAY DIFFRACTIONr_nbd_refined0.1950.21698
X-RAY DIFFRACTIONr_nbd_other0.2480.210060
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.25797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.08725695
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74739108
X-RAY DIFFRACTIONr_scbond_it1.2123195
X-RAY DIFFRACTIONr_scangle_it1.96832958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
1901medium positional0.10.5
2915loose positional0.415
1901medium thermal0.722
2915loose thermal1.1710
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 186
Rwork0.258 3859
Refinement TLS params.

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

IDL11 (°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)
10.1871-0.02420.12140.53820.11310.28810.02830.0015-0.0168-0.0518-0.0182-0.0141-0.032-0.0162-0.01010.01490.0096-0.00760.02940.00140.00562.758527.703318.1999
20.53810.07470.20110.9891-0.02340.30130.00420.0586-0.03-0.12170.0152-0.07720.05090.0367-0.01940.0298-0.0062-0.02050.04090.01360.020922.8464-18.198526.3915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 5819 - 581
2X-RAY DIFFRACTION2BB9 - 5819 - 581

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