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- PDB-6e07: Crystal structure of Canton G6PD in complex with structural NADP -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 60000000
TitleCrystal structure of Canton G6PD in complex with structural NADP
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / G6PD / NADP
Function / homology
Function and homology information


pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / negative regulation of cell growth involved in cardiac muscle cell development / NADPH regeneration ...pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / negative regulation of cell growth involved in cardiac muscle cell development / NADPH regeneration / glucose 6-phosphate metabolic process / NADP+ metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / erythrocyte maturation / cholesterol biosynthetic process / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / glutathione metabolic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / centriolar satellite / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRahighi, S. / Mochly-Rosen, D. / Wakatsuki, S.
CitationJournal: Nat Commun / Year: 2018
Title: Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator.
Authors: Hwang, S. / Mruk, K. / Rahighi, S. / Raub, A.G. / Chen, C.H. / Dorn, L.E. / Horikoshi, N. / Wakatsuki, S. / Chen, J.K. / Mochly-Rosen, D.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 25, 2018ID: 5VG5
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
F: Glucose-6-phosphate 1-dehydrogenase
N: Glucose-6-phosphate 1-dehydrogenase
Q: Glucose-6-phosphate 1-dehydrogenase
T: Glucose-6-phosphate 1-dehydrogenase
W: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,68653
Polymers474,3088
Non-polymers9,37845
Water9,674537
1
L: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,26717
Polymers118,5772
Non-polymers2,69015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-44 kcal/mol
Surface area39770 Å2
MethodPISA
2
F: Glucose-6-phosphate 1-dehydrogenase
W: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,89913
Polymers118,5772
Non-polymers2,32111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-47 kcal/mol
Surface area40160 Å2
MethodPISA
3
N: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,89913
Polymers118,5772
Non-polymers2,32111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-40 kcal/mol
Surface area39730 Å2
MethodPISA
4
Q: Glucose-6-phosphate 1-dehydrogenase
T: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,62210
Polymers118,5772
Non-polymers2,0458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-42 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.120, 206.250, 211.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21C
12L
22F
13L
23N
14L
24Q
15L
25T
16L
26W
17L
27B
18C
28F
19C
29N
110C
210Q
111C
211T
112C
212W
113C
213B
114F
214N
115F
215Q
116F
216T
117F
217W
118F
218B
119N
219Q
120N
220T
121N
221W
122N
222B
123Q
223T
124Q
224W
125Q
225B
126T
226W
127T
227B
128W
228B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPROLA28 - 51228 - 512
21GLNGLNPROPROCB28 - 51228 - 512
12GLNGLNHISHISLA28 - 51328 - 513
22GLNGLNHISHISFC28 - 51328 - 513
13GLNGLNHISHISLA28 - 51328 - 513
23GLNGLNHISHISND28 - 51328 - 513
14GLNGLNPROPROLA28 - 51228 - 512
24GLNGLNPROPROQE28 - 51228 - 512
15GLNGLNHISHISLA28 - 51328 - 513
25GLNGLNHISHISTF28 - 51328 - 513
16GLNGLNHISHISLA28 - 51328 - 513
26GLNGLNHISHISWG28 - 51328 - 513
17SERSERPROPROLA29 - 51229 - 512
27SERSERPROPROBH29 - 51229 - 512
18GLNGLNPROPROCB28 - 51228 - 512
28GLNGLNPROPROFC28 - 51228 - 512
19GLNGLNPROPROCB28 - 51228 - 512
29GLNGLNPROPROND28 - 51228 - 512
110GLNGLNPROPROCB28 - 51228 - 512
210GLNGLNPROPROQE28 - 51228 - 512
111GLNGLNPROPROCB28 - 51228 - 512
211GLNGLNPROPROTF28 - 51228 - 512
112GLNGLNPROPROCB28 - 51228 - 512
212GLNGLNPROPROWG28 - 51228 - 512
113SERSERPROPROCB29 - 51229 - 512
213SERSERPROPROBH29 - 51229 - 512
114GLNGLNHISHISFC28 - 51328 - 513
214GLNGLNHISHISND28 - 51328 - 513
115GLNGLNPROPROFC28 - 51228 - 512
215GLNGLNPROPROQE28 - 51228 - 512
116GLNGLNHISHISFC28 - 51328 - 513
216GLNGLNHISHISTF28 - 51328 - 513
117GLNGLNHISHISFC28 - 51328 - 513
217GLNGLNHISHISWG28 - 51328 - 513
118SERSERPROPROFC29 - 51229 - 512
218SERSERPROPROBH29 - 51229 - 512
119GLNGLNPROPROND28 - 51228 - 512
219GLNGLNPROPROQE28 - 51228 - 512
120GLNGLNHISHISND28 - 51328 - 513
220GLNGLNHISHISTF28 - 51328 - 513
121GLNGLNHISHISND28 - 51328 - 513
221GLNGLNHISHISWG28 - 51328 - 513
122SERSERPROPROND29 - 51229 - 512
222SERSERPROPROBH29 - 51229 - 512
123GLNGLNPROPROQE28 - 51228 - 512
223GLNGLNPROPROTF28 - 51228 - 512
124GLNGLNPROPROQE28 - 51228 - 512
224GLNGLNPROPROWG28 - 51228 - 512
125SERSERPROPROQE29 - 51229 - 512
225SERSERPROPROBH29 - 51229 - 512
126GLNGLNHISHISTF28 - 51328 - 513
226GLNGLNHISHISWG28 - 51328 - 513
127SERSERPROPROTF29 - 51229 - 512
227SERSERPROPROBH29 - 51229 - 512
128SERSERPROPROWG29 - 51229 - 512
228SERSERPROPROBH29 - 51229 - 512

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 59288.547 Da / Num. of mol.: 8 / Mutation: R459L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M AMMONIUM CITRATE TRIBASIC 20% W/V PEG 3350 0.5 MM AG1, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50.01 Å / Num. obs: 171050 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.445 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8374 / % possible all: 100

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0216refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VFL

5vfl
PDB Unreleased entry


Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 21.074 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.504 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21132 8556 5 %RANDOM
Rwork0.18732 ---
obs0.1885 162393 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.785 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å20 Å2
2--0.88 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31554 0 598 537 32689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01932916
X-RAY DIFFRACTIONr_bond_other_d0.0020.0230067
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.97144558
X-RAY DIFFRACTIONr_angle_other_deg0.882369732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29653881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67123.751640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.205155611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.77415248
X-RAY DIFFRACTIONr_chiral_restr0.1030.24742
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02136173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027035
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_it1.8453.46215548
X-RAY DIFFRACTIONr_mcbond_other1.8443.46115547
X-RAY DIFFRACTIONr_mcangle_it3.0915.18719421
X-RAY DIFFRACTIONr_mcangle_other3.0915.18719422
X-RAY DIFFRACTIONr_scbond_it2.323.81217368
X-RAY DIFFRACTIONr_scbond_other2.323.81217368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7265.60325138
X-RAY DIFFRACTIONr_long_range_B_refined5.56240.10235836
X-RAY DIFFRACTIONr_long_range_B_other5.5640.09235821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L157870.09
12C157870.09
21L158070.09
22F158070.09
31L158310.09
32N158310.09
41L157360.09
42Q157360.09
51L157680.09
52T157680.09
61L156920.09
62W156920.09
71L157350.09
72B157350.09
81C159330.08
82F159330.08
91C158610.08
92N158610.08
101C158470.08
102Q158470.08
111C159490.07
112T159490.07
121C158620.08
122W158620.08
131C159070.08
132B159070.08
141F159460.08
142N159460.08
151F159720.07
152Q159720.07
161F160450.07
162T160450.07
171F158420.08
172W158420.08
181F158680.07
182B158680.07
191N157820.09
192Q157820.09
201N158720.08
202T158720.08
211N158310.09
212W158310.09
221N159650.07
222B159650.07
231Q158140.08
232T158140.08
241Q156980.09
242W156980.09
251Q158410.08
252B158410.08
261T159380.08
262W159380.08
271T158400.08
272B158400.08
281W158120.08
282B158120.08
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 689 -
Rwork0.336 11812 -
obs--99.97 %
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)
10.85080.0749-0.20680.6802-0.35671.8535-0.0662-0.0956-0.0117-0.0579-0.1012-0.29880.08920.54080.16740.09210.00160.00620.16860.04990.148235.03717.93515.36
21.3169-0.89880.47631.3863-0.40810.4772-0.1805-0.18290.30760.19730.1073-0.1201-0.2467-0.04930.07320.22970.0414-0.07420.0616-0.0650.12040.26652.67433.307
30.88840.27620.11811.23740.08990.89880.00790.14190.1701-0.1664-0.06010.188-0.09750.00380.05220.12850.03230.01670.0540.01750.06449.9033.524-37.235
41.8144-0.2327-0.18060.67270.18680.7964-0.0138-0.0937-0.1462-0.06720.01930.42220.0238-0.3526-0.00560.134-0.0403-0.11470.23460.09730.3243-28.98515.41528.62
50.7275-0.0043-0.32651.65110.44661.4269-0.0095-0.1109-0.04080.05140.169-0.4871-0.02580.363-0.15950.16720.06410.00640.1245-0.05140.18338.771-21.733-8.91
60.80160.17690.04861.4318-0.15580.7569-0.0810.0224-0.3293-0.17520.05160.08760.2404-0.20140.02950.3049-0.03680.10120.1462-0.08160.284412.768-62.239-29.499
70.84450.41720.00891.23990.06980.9658-0.0198-0.0263-0.0705-0.0953-0.01910.52870.2743-0.28540.03890.2757-0.06580.04960.1258-0.01710.4499-25.071-32.294-21.887
80.883-0.28240.07871.11110.091.3833-0.0501-0.1639-0.29610.14330.15340.07340.3710.0881-0.10340.18930.0325-0.04180.10760.08990.142713.302-10.29646.152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L28 - 513
2X-RAY DIFFRACTION2C28 - 514
3X-RAY DIFFRACTION3F28 - 513
4X-RAY DIFFRACTION4N28 - 513
5X-RAY DIFFRACTION5Q27 - 513
6X-RAY DIFFRACTION6T28 - 513
7X-RAY DIFFRACTION7W28 - 513
8X-RAY DIFFRACTION8B29 - 513

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