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- PDB-2uuh: Crystal structure of Human Leukotriene C4 Synthase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2uuh
TitleCrystal structure of Human Leukotriene C4 Synthase in complex with substrate glutathione
ComponentsLEUKOTRIENE C4 SYNTHASE
KeywordsLYASE / MEMBRANE PROTEIN / LEUKOTRIENE SIGNALLING / MAPEG / HUMAN / LTC4S / ENZYME / TRIMER / MEMBRANE / LEUKOTRIENE BIOSYNTHESIS / EICOSANOID / GLUTATHIONE / TRANSMEMBRANE
Function / homology
Function and homology information


Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process ...Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process / glutathione peroxidase activity / nuclear outer membrane / long-chain fatty acid biosynthetic process / glutathione transferase activity / enzyme activator activity / nuclear envelope / nuclear membrane / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / identical protein binding
Similarity search - Function
5-lipoxygenase-activating protein / FLAP/GST2/LTC4S, conserved site / FLAP/GST2/LTC4S family signature. / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / NICKEL (II) ION / PALMITOLEIC ACID / PALMITIC ACID / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMartinez Molina, D. / Wetterholm, A. / Kohl, A. / McCarthy, A.A. / Niegowski, D. / Ohlson, E. / Hammarberg, T. / Eshaghi, S. / Haeggstrom, J.Z. / Nordlund, P.
CitationJournal: Nature / Year: 2007
Title: Structural Basis for Synthesis of Inflammatory Mediators by Human Leukotriene C4 Synthase.
Authors: Martinez Molina, D. / Wetterholm, A. / Kohl, A. / Mccarthy, A.A. / Niegowski, D. / Ohlson, E. / Hammarberg, T. / Eshaghi, S. / Haeggstrom, J.Z. / Nordlund, P.
History
DepositionMar 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 7, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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: LEUKOTRIENE C4 SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,97912
Polymers17,4121
Non-polymers2,56811
Water2,198122
1
A: LEUKOTRIENE C4 SYNTHASE
hetero molecules

A: LEUKOTRIENE C4 SYNTHASE
hetero molecules

A: LEUKOTRIENE C4 SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,93836
Polymers52,2353
Non-polymers7,70433
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12240 Å2
ΔGint-99.7 kcal/mol
Surface area25240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)169.940, 169.940, 169.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-1147-

NI

21A-1148-

NI

31A-2021-

HOH

41A-2022-

HOH

51A-2042-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein LEUKOTRIENE C4 SYNTHASE / / LEUKOTRIENE-C(4) SYNTHASE / LTC4 SYNTHASE


Mass: 17411.545 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZ / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: Q16873, leukotriene-C4 synthase
#3: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 132 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-PAM / PALMITOLEIC ACID / Palmitoleic acid


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#6: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H32O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 5.07 Å3/Da / Density % sol: 80 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8733
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8733 Å / Relative weight: 1
ReflectionResolution: 1.51→51.23 Å / Num. obs: 47317 / % possible obs: 99.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.8
Reflection shellHighest resolution: 2.15 Å / Redundancy: 5 % / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→49.03 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.431 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1129 5.1 %RANDOM
Rwork0.183 ---
obs0.185 20920 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.52 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 123 122 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211346
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4852.0331811
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.19419.80852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50515182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2791513
X-RAY DIFFRACTIONr_chiral_restr0.2160.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02963
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.2583
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2892
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3830.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.311.5777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93521199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3543637
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7934.5610
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 93 -
Rwork0.245 1544 -
obs--100 %
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)
143.75422.5082-4.829714.5336-2.56358.42650.41250.03420.04640.5494-0.378-0.38590.47180.7522-0.03450.0263-0.0504-0.17430.01320.0166-0.002638.76130.794337.1686
21.63691.49431.45862.62481.89193.76510.0517-0.006-0.25080.1396-0.0663-0.05010.5843-0.15390.01460.0778-0.03040.01120.021-0.02230.07818.69174.788121.1784
31.32931.1540.82622.48561.28991.28190.047-0.1247-0.03430.1694-0.03260.09120.1021-0.1147-0.01430.0402-0.0427-0.00760.0368-0.00640.037413.655314.203529.6632
40.72753.78020.623219.73392.92311.6059-0.1412-0.03550.23190.0911-0.01961.1691-0.2654-0.150.16080.09480.0341-0.03160.1006-0.06390.123211.767239.243935.7931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 4
2X-RAY DIFFRACTION2A5 - 47
3X-RAY DIFFRACTION3A48 - 108
4X-RAY DIFFRACTION4A109 - 145

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