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

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Basic information

Entry
Database: PDB / ID: 2hu5
TitleBinding of inhibitors by Acylaminoacyl-peptidase
ComponentsAcylamino-acid-releasing enzymeAcylaminoacyl-peptidase
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 / 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
GLYCINE / PHENYLALANINE / Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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)127,15811
Polymers126,2172
Non-polymers9419
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-19 kcal/mol
Surface area37520 Å2
MethodPISA
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 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
451A
461B
471A
481B
491A
501B
511A
521B
531A
541B
551A
561B
571A
581B
591A
601B
611A
621B

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
11SERSERILEILEAA10 - 1210 - 12
21SERSERILEILEBB10 - 1210 - 12
32ASPASPGLUGLUAA15 - 1715 - 17
42ASPASPGLUGLUBB15 - 1715 - 17
53LEULEUALAALAAA19 - 2119 - 21
63LEULEUALAALABB19 - 2119 - 21
74GLUGLULEULEUAA23 - 3723 - 37
84GLUGLULEULEUBB23 - 3723 - 37
95VALVALTYRTYRAA39 - 5139 - 51
105VALVALTYRTYRBB39 - 5139 - 51
116GLYGLYPROPROAA53 - 7053 - 70
126GLYGLYPROPROBB53 - 7053 - 70
137GLYGLYSERSERAA73 - 9873 - 98
147GLYGLYSERSERBB73 - 9873 - 98
158PROPROGLYGLYAA100 - 121100 - 121
168PROPROGLYGLYBB100 - 121100 - 121
179ALAALATHRTHRAA123 - 130123 - 130
189ALAALATHRTHRBB123 - 130123 - 130
1910VALVALALAALAAA134 - 148134 - 148
2010VALVALALAALABB134 - 148134 - 148
2111LEULEUGLYGLYAA150 - 161150 - 161
2211LEULEUGLYGLYBB150 - 161150 - 161
2312LEULEUSERSERAA163 - 180163 - 180
2412LEULEUSERSERBB163 - 180163 - 180
2513SERSERPHEPHEAA184 - 190184 - 190
2613SERSERPHEPHEBB184 - 190184 - 190
2714SERSERPHEPHEAA192 - 197192 - 197
2814SERSERPHEPHEBB192 - 197192 - 197
2915ALAALATHRTHRAA200 - 214200 - 214
3015ALAALATHRTHRBB200 - 214200 - 214
3116ALAALAPHEPHEAA218 - 240218 - 240
3216ALAALAPHEPHEBB218 - 240218 - 240
3317TYRTYRTRPTRPAA243 - 291243 - 291
3417TYRTYRTRPTRPBB243 - 291243 - 291
3518LEULEULEULEUAA295 - 318295 - 318
3618LEULEULEULEUBB295 - 318295 - 318
3719ARGARGALAALAAA327 - 331327 - 331
3819ARGARGALAALABB327 - 331327 - 331
3920LEULEUVALVALAA335 - 338335 - 338
4020LEULEUVALVALBB335 - 338335 - 338
4121SERSERVALVALAA340 - 350340 - 350
4221SERSERVALVALBB340 - 350340 - 350
4322SERSERALAALAAA353 - 427353 - 427
4422SERSERALAALABB353 - 427353 - 427
4523GLUGLUTYRTYRAA432 - 478432 - 478
4623GLUGLUTYRTYRBB432 - 478432 - 478
4724LEULEUSERSERAA480 - 496480 - 496
4824LEULEUSERSERBB480 - 496480 - 496
4925ILEILEMETMETAA499 - 500499 - 500
5025ILEILEMETMETBB499 - 500499 - 500
5126SERSERPROPROAA502 - 505502 - 505
5226SERSERPROPROBB502 - 505502 - 505
5327ASNASNASPASPAA507 - 510507 - 510
5427ASNASNASPASPBB507 - 510507 - 510
5528ILEILEPHEPHEAA512 - 546512 - 546
5628ILEILEPHEPHEBB512 - 546512 - 546
5729ALAALATHRTHRAA548 - 560548 - 560
5829ALAALATHRTHRBB548 - 560548 - 560
5930GLUGLULYSLYSAA562 - 566562 - 566
6030GLUGLULYSLYSBB562 - 566562 - 566
6131LEULEUGLUGLUAA568 - 580568 - 580
6231LEULEUGLUGLUBB568 - 580568 - 580
DetailsThe biological assembly is the dimer in the asymmetric unit.

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Components

#1: Protein Acylamino-acid-releasing enzyme / Acylaminoacyl-peptidase / 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 / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-PHE / PHENYLALANINE / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
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, 10% DMSO, 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: May 18, 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→19.726 Å / Num. obs: 67288 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.12
Reflection shellResolution: 2→2.1 Å / Rmerge(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
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VE6

1ve6


Resolution: 2→19.726 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.22441 3377 5 %RANDOM
Rwork0.18147 ---
all0.18363 63906 --
obs0.18363 63906 89.26 %-
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: 17.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: LAST / Resolution: 2→19.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8658 0 62 332 9052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0218935
X-RAY DIFFRACTIONr_bond_other_d0.0020.028304
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.97212115
X-RAY DIFFRACTIONr_angle_other_deg0.762319194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46951160
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_restr0.0710.21345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210111
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021883
X-RAY DIFFRACTIONr_nbd_refined0.1940.21926
X-RAY DIFFRACTIONr_nbd_other0.2480.210742
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.26095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4721.55704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8829121
X-RAY DIFFRACTIONr_scbond_it1.55133231
X-RAY DIFFRACTIONr_scangle_it2.6174.52988
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
2988medium positional0.150.5
4415loose positional0.345
2988medium thermal0.592
4415loose thermal1.0110
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 115
Rwork0.299 2554
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)
10.43810.1380.16111.04370.15210.57330.01030.01850.0045-0.05340.0006-0.0263-0.05950.0007-0.01090.02350.0182-0.01960.05560.00240.02372.73227.586418.2487
20.92830.14180.26931.608-0.00390.4527-0.00650.1397-0.0695-0.22290.027-0.08310.07230.055-0.02050.0661-0.0089-0.03110.09580.01580.052222.7987-17.79526.414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 5819 - 581
2X-RAY DIFFRACTION2BB8 - 5828 - 582

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