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

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Basic information

Entry
Database: PDB / ID: 7nbd
TitleCrystal structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen.
ComponentsSerine racemase
KeywordsISOMERASE / Racemase / XChem / Inhibitor
Function / homology
Function and homology information


: / D-serine biosynthetic process / serine racemase / threonine racemase activity / 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 ...: / D-serine biosynthetic process / serine racemase / threonine racemase activity / 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
[4-(1H-benzimidazol-1-yl)phenyl]methanol / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.865 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: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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)152,68632
Polymers149,8234
Non-polymers2,86228
Water18,9701053
1
AAA: Serine racemase
CCC: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,54017
Polymers74,9122
Non-polymers1,62815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Serine racemase
DDD: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,14615
Polymers74,9122
Non-polymers1,23413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.012, 154.846, 85.451
Angle α, β, γ (deg.)90.000, 98.043, 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: 37455.863 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, 1081 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Mutation: C2D, C6D
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P
Details: Cofactor pyridoxal-5'-phosphate (PLP, LLP) is covalently bound to lysine 56
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-JFS / [4-(1H-benzimidazol-1-yl)phenyl]methanol


Mass: 224.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1053 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
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: 0.91578 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: 0.91578 Å / Relative weight: 1
ReflectionResolution: 1.86→84.61 Å / Num. obs: 96340 / % possible obs: 94 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.86→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 12195 / CC1/2: 0.47 / % possible all: 82

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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: 1.865→84.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.478 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.171 / ESU R Free: 0.142 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2074 4830 5.016 %
Rwork0.1762 91467 -
all0.178 --
obs-96297 93.91 %
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: 37.903 Å2
Baniso -1Baniso -2Baniso -3
1--0.245 Å2-0 Å20.231 Å2
2--0.293 Å2-0 Å2
3----0.109 Å2
Refinement stepCycle: LAST / Resolution: 1.865→84.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9472 0 179 1053 10704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01210638
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.62514613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16251429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24924.508417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.291151685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3431532
X-RAY DIFFRACTIONr_chiral_restr0.1140.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028074
X-RAY DIFFRACTIONr_nbd_refined0.2530.25665
X-RAY DIFFRACTIONr_nbtor_refined0.3140.27009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2888
X-RAY DIFFRACTIONr_metal_ion_refined0.1710.227
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3260.238
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1170.22
X-RAY DIFFRACTIONr_mcbond_it2.2793.045537
X-RAY DIFFRACTIONr_mcangle_it3.4074.5297027
X-RAY DIFFRACTIONr_scbond_it3.1893.3085101
X-RAY DIFFRACTIONr_scangle_it4.7074.8547586
X-RAY DIFFRACTIONr_lrange_it11.18760.36555074
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.865-1.9130.3243080.30662390.30775780.6570.65886.39480.302
1.913-1.9650.2792860.27653470.27673050.8040.79677.11160.263
1.965-2.0220.2913620.25266920.25472310.8120.82997.55220.236
2.022-2.0850.2712430.23847460.23969870.8630.8671.4040.22
2.085-2.1530.2273340.20962190.2166970.8990.90397.84980.19
2.153-2.2280.2533090.20160790.20465360.8910.90797.73560.18
2.228-2.3120.2183240.18658600.18863240.9190.9397.78620.164
2.312-2.4070.2243160.17256490.17560830.9260.94298.06020.15
2.407-2.5140.2132860.17154230.17358200.9340.94398.09280.149
2.514-2.6360.2132740.16851690.1755350.9310.94698.33790.144
2.636-2.7790.1952580.15949570.16153050.9490.95998.30350.139
2.779-2.9470.1822400.15147030.15350220.9570.96298.42690.134
2.947-3.150.1932440.15244150.15447120.9510.9698.87520.139
3.15-3.4020.1922230.15241280.15444060.9520.96498.75170.143
3.402-3.7270.1762070.15437530.15540290.960.96998.28740.151
3.727-4.1650.1771770.14733850.14936400.970.97397.85710.149
4.165-4.8080.1491580.1430510.1432750.9710.97597.98470.149
4.808-5.8840.2381260.18425430.18627060.9410.95598.63270.194
5.884-8.3010.226990.21719870.21821290.9440.95397.98030.233
8.301-84.610.236560.20811220.20912000.9470.95898.16670.245
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)
10.0512-0.00570.46842.79230.50584.69360.00250.034-0.0061-0.58620.2131-0.0076-0.24990.3434-0.21560.1485-0.02910.04790.08480.01130.0967-8.7034-14.557225.2142
20.5027-0.01720.05260.40310.01760.39830.0376-0.0155-0.01520.02190.0039-0.09010.021-0.0251-0.04150.00890.0047-0.00580.02220.0140.050810.4176-25.933242.1128
35.5497-1.6226-0.82558.81384.81084.4482-0.0506-0.3516-0.15230.9761-0.0862-0.0975-0.11080.14510.13680.3518-0.0894-0.07150.08570.07420.0803-17.0146-71.382491.1225
40.3717-0.2397-0.05521.4091-0.03830.5801-0.00810.00110.04720.02270.0246-0.2190.0737-0.0602-0.01650.04290.0061-0.00520.01920.00190.03635.9377-60.705879.2475
51.6913-1.4808-0.46652.64210.67933.14660.08450.1634-0.0067-0.4076-0.20870.0166-0.0145-0.27160.12420.14820.0427-0.02130.0488-0.01510.014919.8054-69.064630.2005
60.55930.3218-0.13231.4128-0.24690.2077-0.02080.0290.10250.00150.06940.210.06790.003-0.04860.0627-0.0076-0.01280.01160.01490.0397-5.2431-57.900941.561
70.2547-0.4304-1.06234.3517-1.07897.3804-0.1020.0901-0.0480.7326-0.20560.29260.1814-0.30650.30760.1967-0.07650.14460.0659-0.04450.15869.882-17.345792.8154
80.6017-0.177-0.02630.3786-0.08260.58870.036-0.025-0.0127-0.0081-0.02080.07580.01640.0126-0.01530.0066-0.00610.00310.066-0.01480.0193-10.1105-29.053775.7474
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 DIFFRACTION3ALLBBB101 - 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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