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- PDB-5wqk: Crystal structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) i... -

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Basic information

Entry
Database: PDB / ID: 5wqk
TitleCrystal structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in complex with compound1
ComponentsSulfurtransferase
KeywordsTRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


3-mercaptopyruvate sulfurtransferase / Degradation of cysteine and homocysteine / 3-mercaptopyruvate sulfurtransferase activity / hydrogen sulfide biosynthetic process / thiosulfate sulfurtransferase activity / transsulfuration / spinal cord development / liver development / kidney development / mitochondrial inner membrane ...3-mercaptopyruvate sulfurtransferase / Degradation of cysteine and homocysteine / 3-mercaptopyruvate sulfurtransferase activity / hydrogen sulfide biosynthetic process / thiosulfate sulfurtransferase activity / transsulfuration / spinal cord development / liver development / kidney development / mitochondrial inner membrane / neuron projection / synapse / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
Sulfurtransferase TST/MPST-like / Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Sulfurtransferase TST/MPST-like / Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7NC / 3-mercaptopyruvate sulfurtransferase / 3-mercaptopyruvate sulfurtransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSuwanai, Y. / Toma-Fukai, S. / Shimizu, T.
CitationJournal: Sci Rep / Year: 2017
Title: Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-site Cysteine Persulfide
Authors: Hanaoka, K. / Sasakura, K. / Suwanai, Y. / Toma-Fukai, S. / Shimamoto, K. / Takano, Y. / Shibuya, N. / Terai, T. / Komatsu, T. / Ueno, T. / Ogasawara, Y. / Tsuchiya, Y. / Watanabe, Y. / ...Authors: Hanaoka, K. / Sasakura, K. / Suwanai, Y. / Toma-Fukai, S. / Shimamoto, K. / Takano, Y. / Shibuya, N. / Terai, T. / Komatsu, T. / Ueno, T. / Ogasawara, Y. / Tsuchiya, Y. / Watanabe, Y. / Kimura, H. / Wang, C. / Uchiyama, M. / Kojima, H. / Okabe, T. / Urano, Y. / Shimizu, T. / Nagano, T.
History
DepositionNov 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfurtransferase
B: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1068
Polymers65,3932
Non-polymers7136
Water7,512417
1
A: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0534
Polymers32,6971
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area13760 Å2
MethodPISA
2
B: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0534
Polymers32,6971
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.328, 149.686, 54.013
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sulfurtransferase


Mass: 32696.621 Da / Num. of mol.: 2 / Fragment: UNP residues 5-297 / Mutation: C65S, C255S, C264S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mpst, mCG_13337 / Production host: Escherichia coli (E. coli) / References: UniProt: Q505N7, UniProt: Q99J99*PLUS
#2: Chemical ChemComp-7NC / 4-methyl-2-(2-naphthalen-1-yl-2-oxidanylidene-ethyl)sulfanyl-1~{H}-pyrimidin-6-one


Mass: 310.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14N2O2S
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3,350, HEPES-NaOH, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 59621 / % possible obs: 98 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.688 / CC1/2: 0.66 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.491 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22085 2924 4.9 %RANDOM
Rwork0.17474 ---
obs0.17699 56656 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.923 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0.14 Å2
2--0.21 Å20 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 48 417 5076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194977
X-RAY DIFFRACTIONr_bond_other_d0.0020.024564
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9516780
X-RAY DIFFRACTIONr_angle_other_deg0.907310526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92523.277238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57515783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1321537
X-RAY DIFFRACTIONr_chiral_restr0.1170.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021228
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_it1.391.242435
X-RAY DIFFRACTIONr_mcbond_other1.3731.2392433
X-RAY DIFFRACTIONr_mcangle_it2.0631.8513070
X-RAY DIFFRACTIONr_mcangle_other2.0621.8513071
X-RAY DIFFRACTIONr_scbond_it1.9261.4332542
X-RAY DIFFRACTIONr_scbond_other1.9261.4332542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0422.0663711
X-RAY DIFFRACTIONr_long_range_B_refined4.19410.1295809
X-RAY DIFFRACTIONr_long_range_B_other4.19310.135810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 206 -
Rwork0.239 4028 -
obs--94.24 %

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