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- PDB-7nbh: Crystal structure of human serine racemase in complex with DSiP f... -

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Basic information

Entry
Database: PDB / ID: 7nbh
TitleCrystal structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen.
ComponentsSerine racemase
KeywordsISOMERASE / Racemase / XChem / Inhibitor
Function / homology
Function and homology information


: / threonine racemase activity / D-serine biosynthetic process / serine racemase / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase activity / D-serine metabolic process ...: / threonine racemase activity / D-serine biosynthetic process / serine racemase / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase activity / D-serine metabolic process / Serine metabolism / pyruvate biosynthetic process / L-serine metabolic process / glycine binding / PDZ domain binding / apical part of cell / pyridoxal phosphate binding / response to lipopolysaccharide / response to xenobiotic stimulus / neuronal cell body / calcium ion binding / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chem-W0D / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKoulouris, C.R. / Roe, S.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Citation
Journal: Commun Biol / Year: 2022
Title: Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.
Authors: Koulouris, C.R. / Gardiner, S.E. / Harris, T.K. / Elvers, K.T. / Mark Roe, S. / Gillespie, J.A. / Ward, S.E. / Grubisha, O. / Nicholls, R.A. / Atack, J.R. / Bax, B.D.
#1: Journal: Biorxiv / Year: 2021
Title: Tyrosine 121 moves revealing a druggable pocket that couples catalysis to ATP-binding in serine racemase
Authors: Koulouris, C.R. / Gardiner, S.E. / Harris, T.K. / Elvers, K.T. / Roe, S.M. / Gillespie, J.A. / Ward, S.E. / Grubisha, O. / Nicholls, R.A. / Atack, J.R. / Bax, B.D.
History
DepositionJan 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 4, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Serine racemase
BBB: Serine racemase
CCC: Serine racemase
DDD: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,57351
Polymers150,7364
Non-polymers3,83747
Water17,565975
1
AAA: Serine racemase
DDD: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,86531
Polymers75,3682
Non-polymers2,49729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-57 kcal/mol
Surface area26070 Å2
MethodPISA
2
BBB: Serine racemase
CCC: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,70820
Polymers75,3682
Non-polymers1,34018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-59 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.180, 154.880, 85.480
Angle α, β, γ (deg.)90.000, 98.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Serine racemase / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase


Mass: 37683.977 Da / Num. of mol.: 4 / Mutation: C2D, C6D
Source method: isolated from a genetically manipulated source
Details: Cofactor pyridoxal-5'-phosphate (PLP, LLP) is covalently bound to lysine 56
Source: (gene. exp.) Homo sapiens (human) / Gene: SRR / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (DE3)-RIL
References: UniProt: Q9GZT4, serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase

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Non-polymers , 9 types, 1022 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-W0D / N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide


Mass: 241.245 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 mM MES pH 6.2 100 mM calcium chloride 5% ethylene glycol 20% PEG Smear Broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.77→51.6 Å / Num. obs: 116780 / % possible obs: 97.1 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.098 / Net I/σ(I): 8.2
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1 / Num. unique obs: 8546 / CC1/2: 0.302 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZUJ

6zuj


Resolution: 1.77→47.752 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.166 / SU B: 5.352 / SU ML: 0.098 / Average fsc free: 0.8862 / Average fsc work: 0.8948 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.118 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2018 5859 5.019 %
Rwork0.1694 110878 -
all0.171 --
obs-116737 97.001 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 35.476 Å2
Baniso -1Baniso -2Baniso -3
1--0.385 Å2-0 Å20.29 Å2
2--0.588 Å20 Å2
3----0.274 Å2
Refinement stepCycle: LAST / Resolution: 1.77→47.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9435 0 250 975 10660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01210816
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.62814845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75551450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99924.309427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.906151718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4611532
X-RAY DIFFRACTIONr_chiral_restr0.1160.21453
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028237
X-RAY DIFFRACTIONr_nbd_refined0.2210.25840
X-RAY DIFFRACTIONr_nbtor_refined0.310.27302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2875
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.248
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.238
X-RAY DIFFRACTIONr_mcbond_it2.3432.7615546
X-RAY DIFFRACTIONr_mcangle_it3.3324.117081
X-RAY DIFFRACTIONr_scbond_it3.4463.1755270
X-RAY DIFFRACTIONr_scangle_it4.8634.6117764
X-RAY DIFFRACTIONr_lrange_it10.56555.55855196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.8160.3464320.3358103X-RAY DIFFRACTION96.1257
1.816-1.8660.3124410.3127938X-RAY DIFFRACTION96.51
1.866-1.920.2913860.2717786X-RAY DIFFRACTION96.7673
1.92-1.9790.2663910.2427459X-RAY DIFFRACTION96.9375
1.979-2.0440.2443910.2177291X-RAY DIFFRACTION96.8116
2.044-2.1150.2223810.1967044X-RAY DIFFRACTION96.7679
2.115-2.1950.2173390.1796867X-RAY DIFFRACTION96.634
2.195-2.2850.2013580.1666509X-RAY DIFFRACTION97.225
2.285-2.3860.1993670.1556272X-RAY DIFFRACTION97.2035
2.386-2.5030.1992970.166047X-RAY DIFFRACTION97.2112
2.503-2.6380.2162950.1565780X-RAY DIFFRACTION97.7631
2.638-2.7980.1992930.1565452X-RAY DIFFRACTION97.6211
2.798-2.9910.1952630.1525147X-RAY DIFFRACTION97.6711
2.991-3.230.192660.1484778X-RAY DIFFRACTION97.8468
3.23-3.5380.1912330.1514380X-RAY DIFFRACTION97.5058
3.538-3.9540.162140.1423929X-RAY DIFFRACTION96.3488
3.954-4.5640.1571690.1283480X-RAY DIFFRACTION96.8161
4.564-5.5860.1791630.1492987X-RAY DIFFRACTION97.5534
5.586-7.8830.1981230.1872328X-RAY DIFFRACTION97.8053
7.883-47.7520.181570.171301X-RAY DIFFRACTION97.2083
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)
10.79130.7843-0.40873.04012.18926.40240.00580.16080.336-0.28610.18360.0596-0.00170.5371-0.18930.07220.06020.06780.14560.1190.2035-9.1262-14.94225.1151
20.45590.00640.04920.42970.07260.32260.0302-0.0039-0.01510.0266-0.0003-0.06080.0234-0.0096-0.02990.01620.00370.01680.02040.01260.053210.3665-25.936942.2775
32.63851.2904-0.83721.88930.31090.68580.2578-0.281-0.16910.548-0.2773-0.09570.1475-0.00430.01940.1871-0.0710.00660.11110.06370.0736-16.1674-69.914288.1086
40.5769-0.1135-0.03230.87110.09540.32450.0034-0.03480.03870.02690.0149-0.11180.0416-0.0142-0.01830.06060.00980.00370.01010.00110.01796.0249-60.772879.2548
52.0795-0.55850.36265.3235-1.03492.1550.03830.24350.0271-0.4135-0.01230.10110.0588-0.0807-0.0260.09580.02590.00590.04960.00640.008819.795-68.790930.147
60.59740.1354-0.16560.797-0.23410.3157-0.02780.03220.0771-0.00320.06850.09790.0771-0.026-0.04070.0747-0.0174-0.00130.01160.01110.0243-5.2815-57.94741.7191
72.53320.3839-0.57715.4122-1.07164.30260.1204-0.36070.23210.8376-0.10160.23020.0256-0.1597-0.01880.155-0.06170.05460.1125-0.05760.037210.1456-17.661892.8431
80.5667-0.0651-0.01290.3651-0.14160.50890.01930.0021-0.0206-0.0024-0.00820.0530.02-0.0124-0.01110.0185-0.00690.02030.0413-0.01460.034-10.0972-29.111575.9138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA101 - 150
2X-RAY DIFFRACTION2ALLAAA7 - 55
3X-RAY DIFFRACTION2ALLAAA157 - 295
4X-RAY DIFFRACTION2ALLAAA307 - 315
5X-RAY DIFFRACTION3ALLBBB77 - 150
6X-RAY DIFFRACTION4ALLBBB7 - 55
7X-RAY DIFFRACTION4ALLBBB157 - 295
8X-RAY DIFFRACTION4ALLBBB307 - 315
9X-RAY DIFFRACTION5ALLCCC101 - 150
10X-RAY DIFFRACTION6ALLCCC7 - 55
11X-RAY DIFFRACTION6ALLCCC157 - 295
12X-RAY DIFFRACTION6ALLCCC307 - 315
13X-RAY DIFFRACTION7ALLDDD101 - 150
14X-RAY DIFFRACTION8ALLDDD7 - 55
15X-RAY DIFFRACTION8ALLDDD157 - 295
16X-RAY DIFFRACTION8ALLDDD307 - 315

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