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- PDB-3uy9: Bovine trypsin variant X(tripleGlu217Phe227) in complex with smal... -

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Basic information

Entry
Database: PDB / ID: 3uy9
TitleBovine trypsin variant X(tripleGlu217Phe227) in complex with small molecule inhibitor
ComponentsCationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Trypsin-like serine protease / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsTziridis, A. / Neumann, P. / Kolenko, P. / Stubbs, M.T.
CitationJournal: Biol.Chem. / Year: 2014
Title: Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.
Authors: Tziridis, A. / Rauh, D. / Neumann, P. / Kolenko, P. / Menzel, A. / Brauer, U. / Ursel, C. / Steinmetzer, P. / Sturzebecher, J. / Schweinitz, A. / Steinmetzer, T. / Stubbs, M.T.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Dec 5, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Cationic trypsin
C: Cationic trypsin
D: Cationic trypsin
E: Cationic trypsin
F: Cationic trypsin
G: Cationic trypsin
H: Cationic trypsin
I: Cationic trypsin
J: Cationic trypsin
K: Cationic trypsin
L: Cationic trypsin
M: Cationic trypsin
N: Cationic trypsin
O: Cationic trypsin
P: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,35851
Polymers375,68716
Non-polymers2,67035
Water00
1
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6764
Polymers23,4801
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6764
Polymers23,4801
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6413
Polymers23,4801
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6764
Polymers23,4801
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.069, 98.569, 120.781
Angle α, β, γ (deg.)89.62, 88.85, 103.99
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A
14E
24A
15F
25A
16G
26A
17H
27A
18I
28A
19J
29A
110K
210A
111L
211A
112M
212A
113N
213A
114O
214A
115P
215A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B16 - 245
2111A16 - 245
1121C16 - 245
2121A16 - 245
1131D16 - 245
2131A16 - 245
1141E16 - 245
2141A16 - 245
1151F16 - 245
2151A16 - 245
1161G16 - 245
2161A16 - 245
1171H16 - 245
2171A16 - 245
1181I16 - 245
2181A16 - 245
1191J16 - 2452
2191A16 - 2452
11101K16 - 245
21101A16 - 245
11111L16 - 245
21111A16 - 245
11121M16 - 245
21121A16 - 245
11131N16 - 245
21131A16 - 245
11141O16 - 245
21141A16 - 245
11151P16 - 245
21151A16 - 245

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 23480.467 Da / Num. of mol.: 16
Mutation: N102E, L104Y, Y175S P176S, G177F, Q178Y, S195A, S218E, V228F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00760, trypsin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG8000, 0.3M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.878
11-h,-k,l20.122
ReflectionResolution: 3.22→120.78 Å / Num. obs: 56715 / % possible obs: 89.25 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
AMoREphasing
REFMAC5.5.0110refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V2K

1v2k


Resolution: 3.22→120.78 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0 / SU B: 15.405 / SU ML: 0.262 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TWIN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 568 -RANDOM
Rwork0.2054 ---
all0.2072 56715 --
obs0.2072 56715 89.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å210.56 Å2-5.51 Å2
2---29.61 Å2-5.42 Å2
3---29.72 Å2
Refinement stepCycle: LAST / Resolution: 3.22→120.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26224 0 163 0 26387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02226976
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217584
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.94736608
X-RAY DIFFRACTIONr_angle_other_deg1.028343296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52353552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98525.667960
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26154336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.991532
X-RAY DIFFRACTIONr_chiral_restr0.0880.24064
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0230448
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025024
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.05

Ens-IDAuth asym-IDNumberRms dev position (Å)
1B27310.06
2C27310.05
3D27310.06
4E27310.06
5F27310.06
6G27310.06
7H27310.06
8I27310.06
9J27320.05
10K27310.06
11L27310.06
12M27310.06
13N27310.06
14O27310.06
15P27310.06

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