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- PDB-6i9a: Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibi... -

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Basic information

Entry
Database: PDB / ID: 6i9a
TitlePorphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36
ComponentsLys-gingipain W83
KeywordsHYDROLASE / peptidase inhibitor / custeine peptidase / gingipain / periodontopathogen / periodontal disease / Porphyromonas gingivalis
Function / homology
Function and homology information


gingipain K / hemolysis in another organism / cysteine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular region
Similarity search - Function
Cleaved adhesin / Peptidase C25, gingipain, C-terminal / Cleaved Adhesin Domain / Domain of unknown function (DUF2436) / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain ...Cleaved adhesin / Peptidase C25, gingipain, C-terminal / Cleaved Adhesin Domain / Domain of unknown function (DUF2436) / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 / Gingipain / Peptidase family C25 / Caspase-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Chem-H8E / Lys-gingipain W83
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGomis-Ruth, F.X. / Guevara, T. / Rofdriguez-Banqueri, A.
Citation
Journal: Sci Rep / Year: 2019
Title: Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor.
Authors: Guevara, T. / Rodriguez-Banqueri, A. / Lasica, A.M. / Ksiazek, M. / Potempa, B.A. / Potempa, J. / Gomis-Ruth, F.X.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structural insights unravel the zymogenic mechanism of the virulence factor gingipain K from
Authors: Pomowski, A. / Uson, I. / Nowakowska, Z. / Veillard, F. / Sztukowska, M.N. / Guevara, T. / Goulas, T. / Mizgalska, D. / Nowak, M. / Potempa, B. / Huntington, J.A. / Potempa, J. / Gomis-Rueth, F.X.
#2: Journal: J. Biol. Chem. / Year: 2014
Title: Structure and mechanism of cysteine peptidase gingipain K (Kgp), a major virulence factor of Porphyromonas gingivalis in periodontitis.
Authors: de Diego, I. / Veillard, F. / Sztukowska, M.N. / Guevara, T. / Potempa, B. / Pomowski, A. / Huntington, J.A. / Potempa, J. / Gomis-Rueth, F.X.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Refinement description / Category: pdbx_refine_tls_group / Item: _pdbx_refine_tls_group.pdbx_refine_id
Revision 1.2Mar 27, 2019Group: Data collection / Refinement description / Category: pdbx_refine_tls / Item: _pdbx_refine_tls.pdbx_refine_id
Revision 1.3Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 24, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lys-gingipain W83
B: Lys-gingipain W83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,81525
Polymers102,0262
Non-polymers2,78923
Water28,4641580
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A: Lys-gingipain W83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,33012
Polymers51,0131
Non-polymers1,31711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lys-gingipain W83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,48413
Polymers51,0131
Non-polymers1,47212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.670, 87.050, 129.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lys-gingipain W83 / Lysine specific cysteine protease / Lysine-specific cysteine proteinase / Porphypain / PrtK48


Mass: 51012.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: kgp, prtK, prtP
Production host: Porphyromonas gingivalis ATCC 33277 (bacteria)
References: UniProt: Q51817, gingipain K

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Non-polymers , 8 types, 1603 molecules

#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-H8E / benzyl-N-[(2S)-1-[[(3S)-7-amino-1-(benzylamino)-1,2-dioxoheptan-3-yl]amino]-5-(2-methyl-2-phenylhydrazinyl)-1,5-dioxopentan-2-yl]carbamate


Mass: 630.734 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H42N6O6
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1580 / 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: 2.39 Å3/Da / Density % sol: 48.5 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 8000, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.2→72.2 Å / Num. obs: 290672 / % possible obs: 95.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 10.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Net I/σ(I): 19.6
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.843 / Rrim(I) all: 0.8 / % possible all: 75.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RBM

4rbm


Resolution: 1.2→72.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.972 / SU R Cruickshank DPI: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.037 / SU Rfree Blow DPI: 0.035 / SU Rfree Cruickshank DPI: 0.032
RfactorNum. reflection% reflectionSelection details
Rfree0.148 1120 0.39 %RANDOM
Rwork0.146 ---
obs0.146 290671 95.8 %-
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.0381 Å20 Å20 Å2
2---3.6747 Å20 Å2
3---2.6366 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.2→72.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7048 0 178 1580 8806
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0127734HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1710559HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3509SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1335HARMONIC5
X-RAY DIFFRACTIONt_it7516HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.8
X-RAY DIFFRACTIONt_other_torsion2.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion996SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies49HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10684SEMIHARMONIC4
LS refinement shellResolution: 1.2→1.21 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2375 -0.41 %
Rwork0.1871 5790 -
all0.1873 5814 -
obs--61.04 %
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)
10.2651-0.0156-0.00960.2162-0.03530.38960.0030.01060.0011-0.00960.0050.0088-0.02780.0088-0.0080.01050.00260.00130.01630.00330.01545.2555-17.564-7.5755
20.243-0.05680.0620.10440.18130.30490.00010.00380.0025-0.0071-0.0008-0.00240.00060.00010.00070.0150.0036-0.00710.0183-0.004-0.00038.0087-29.8032-35.0677
30.25320.00920.04340.20110.01250.3740.0092-0.00580.0027-0.006-0.00870.01040.0024-0.0058-0.00050.0121-0.0005-0.00260.01390.00070.0165-3.5231-59.118322.5523
40.1360.011-0.22070.152-0.06120.30230.00010.00570.0046-0.00680.00040.0021-0.00440.0018-0.00050.01340.0010.00420.0191-0.00160.0028.4877-54.2267-4.1604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|229 - 600 A|994 - 1001}
2X-RAY DIFFRACTION2{A|601 - 681}
3X-RAY DIFFRACTION3{B|229 - 600 B|994 - 1001}
4X-RAY DIFFRACTION4{B|601 - 681}

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