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- PDB-2hu8: Binding of inhibitors by Acylaminoacyl peptidase -

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Basic information

Entry
Database: PDB / ID: 2hu8
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 / serine-type peptidase activity / omega peptidase 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
2-AMINOBENZOIC ACID / GLYCINE / PHENYLALANINE / Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Nov 10, 2021Group: 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 2.0Nov 15, 2023Group: 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

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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)126,9408
Polymers126,1852
Non-polymers7556
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-13 kcal/mol
Surface area38540 Å2
MethodPISA
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 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
12A
22B
32A
42B
52A
62B
72A
82B
92A
102B
112A
122B
132A
142B
152A
162B
172A
182B
192A
202B

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSGLYGLYAA24 - 2924 - 29
211LYSLYSGLYGLYBB24 - 2924 - 29
321VALVALVALVALAA31 - 3931 - 39
421VALVALVALVALBB31 - 3931 - 39
531ASNASNTYRTYRAA47 - 5147 - 51
631ASNASNTYRTYRBB47 - 5147 - 51
741VALVALARGARGAA57 - 6157 - 61
841VALVALARGARGBB57 - 6157 - 61
951PROPROHISHISAA63 - 7163 - 71
1051PROPROHISHISBB63 - 7163 - 71
1161GLYGLYTHRTHRAA73 - 13073 - 130
1261GLYGLYTHRTHRBB73 - 13073 - 130
1371VALVALARGARGAA134 - 145134 - 145
1471VALVALARGARGBB134 - 145134 - 145
1581LEULEUGLYGLYAA147 - 161147 - 161
1681LEULEUGLYGLYBB147 - 161147 - 161
1791LEULEUSERSERAA163 - 180163 - 180
1891LEULEUSERSERBB163 - 180163 - 180
19101SERSERPHEPHEAA184 - 190184 - 190
20101SERSERPHEPHEBB184 - 190184 - 190
21111GLYGLYTHRTHRAA193 - 214193 - 214
22111GLYGLYTHRTHRBB193 - 214193 - 214
23121ARGARGSERSERAA219 - 229219 - 229
24121ARGARGSERSERBB219 - 229219 - 229
25131PHEPHETYRTYRAA240 - 243240 - 243
26131PHEPHETYRTYRBB240 - 243240 - 243
27141ALAALAPROPROAA247 - 255247 - 255
28141ALAALAPROPROBB247 - 255247 - 255
29151GLYGLYVALVALAA257 - 278257 - 278
30151GLYGLYVALVALBB257 - 278257 - 278
31161PROPROLEULEUAA281 - 302281 - 302
32161PROPROLEULEUBB281 - 302281 - 302
33171THRTHRGLYGLYAA304 - 320304 - 320
34171THRTHRGLYGLYBB304 - 320304 - 320
112SERSERVALVALAA10 - 1310 - 13
212SERSERVALVALBB10 - 1310 - 13
322ASPASPVALVALAA15 - 2215 - 22
422ASPASPVALVALBB15 - 2215 - 22
532PROPROSERSERAA323 - 344323 - 344
632PROPROSERSERBB323 - 344323 - 344
742VALVALPROPROAA346 - 359346 - 359
842VALVALPROPROBB346 - 359346 - 359
952THRTHRTHRTHRAA362 - 380362 - 380
1052THRTHRTHRTHRBB362 - 380362 - 380
1162ALAALAVALVALAA382 - 472382 - 472
1262ALAALAVALVALBB382 - 472382 - 472
1372TRPTRPSERSERAA474 - 496474 - 496
1472TRPTRPSERSERBB474 - 496474 - 496
1582ILEILEMETMETAA499 - 500499 - 500
1682ILEILEMETMETBB499 - 500499 - 500
1792SERSERPROPROAA502 - 505502 - 505
1892SERSERPROPROBB502 - 505502 - 505
19102ASNASNARGARGAA507 - 581507 - 581
20102ASNASNARGARGBB507 - 581507 - 581

NCS ensembles :
ID
1
2
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: 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 / Anthranilic acid


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


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


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 21, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→19.96 Å / Num. obs: 45009 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.68
Reflection shellResolution: 2.4→2.5 Å / Rmerge(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
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.96 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.26128 2264 5 %RANDOM (as for related pdb entry 2HU5)
Rwork0.2155 ---
all0.21778 42954 --
obs0.21778 42954 99.56 %-
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: 5.952 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.394 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8584 0 50 223 8857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0218861
X-RAY DIFFRACTIONr_bond_other_d0.0010.028217
X-RAY DIFFRACTIONr_angle_refined_deg0.8781.9712043
X-RAY DIFFRACTIONr_angle_other_deg0.887318951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79151162
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_restr0.0550.21349
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021865
X-RAY DIFFRACTIONr_nbd_refined0.1850.31532
X-RAY DIFFRACTIONr_nbd_other0.2420.39111
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.55238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.5419
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.370
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0611.55708
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.10929120
X-RAY DIFFRACTIONr_scbond_it0.26433153
X-RAY DIFFRACTIONr_scangle_it0.4144.52916
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 / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11449tight positional0.020.05
21523tight positional0.030.05
12103medium positional0.280.5
22260medium positional0.330.5
11449tight thermal0.020.5
21523tight thermal0.030.5
12103medium thermal0.12
22260medium thermal0.122
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 153
Rwork0.282 3075
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.89110.0780.24441.06740.0821.6782-0.0609-0.02870.1812-0.0335-0.0118-0.0644-0.20910.00750.07270.1351-0.0029-0.05370.072-0.00280.11546.086740.47519.5147
21.2305-0.23410.62041.748-0.05511.31550.014-0.004-0.0811-0.0204-0.049-0.09050.0982-0.0170.0350.0540.0002-0.0390.06680.01380.0315-1.664213.579517.3314
33.3666-0.03470.88261.9641-0.27320.99130.47010.5977-0.6561-0.4409-0.1321-0.20240.40020.2563-0.33810.48910.0939-0.18830.2344-0.09120.453721.1905-31.124522.4056
43.3399-0.96751.31732.9473-0.38340.93280.06430.38580.2641-0.0715-0.1729-0.48090.05260.16540.10870.1085-0.0015-0.04670.1740.08550.14925.0555-4.731330.3335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA23 - 32123 - 321
2X-RAY DIFFRACTION2AA322 - 582322 - 582
3X-RAY DIFFRACTION2AA8 - 228 - 22
4X-RAY DIFFRACTION3BB23 - 32123 - 321
5X-RAY DIFFRACTION4BB322 - 581322 - 581
6X-RAY DIFFRACTION4BB9 - 229 - 22

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