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- PDB-9rau: Streptococcus pyogenes GapN in complex with pyrimidine-5-amine -

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Basic information

Entry
Database: PDB / ID: 9rau
TitleStreptococcus pyogenes GapN in complex with pyrimidine-5-amine
ComponentsNADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GapN / Fragment screening / Soaking
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function
: / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
pyrimidin-5-amine / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsWirsing, R. / Schindelin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Streptococcus pyogenes GapN in complex with pyrimidine-5-amine
Authors: Wirsing, R. / Schindelin, H.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,89451
Polymers423,6738
Non-polymers5,22143
Water52,6042920
1
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,57925
Polymers211,8374
Non-polymers2,74321
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20490 Å2
ΔGint-207 kcal/mol
Surface area59860 Å2
MethodPISA
2
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,31426
Polymers211,8374
Non-polymers2,47822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20480 Å2
ΔGint-184 kcal/mol
Surface area60280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.764, 98.946, 103.032
Angle α, β, γ (deg.)78.040, 75.630, 67.010
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 52959.152 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: E0F67_08075 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A4U9C786

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Non-polymers , 7 types, 2963 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-T5V / pyrimidin-5-amine


Mass: 95.103 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H5N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2920 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: BisTris buffer pH 6.7 Li2SO4 polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.77→44.22 Å / Num. obs: 310076 / % possible obs: 67.54 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1738 / Rpim(I) all: 0.1045 / Rrim(I) all: 0.2031 / Net I/σ(I): 6.64
Reflection shellResolution: 1.77→1.833 Å / Rmerge(I) obs: 2.187 / Mean I/σ(I) obs: 0.61 / Num. unique obs: 2762 / CC1/2: 0.238 / Rpim(I) all: 1.315 / Rrim(I) all: 2.556

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→44.22 Å / SU ML: 0.2097 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.61
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 11190 4.97 %
Rwork0.1749 213848 -
obs0.1771 225038 67.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.66 Å2
Refinement stepCycle: LAST / Resolution: 1.77→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28368 0 327 2920 31615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429427
X-RAY DIFFRACTIONf_angle_d0.597839951
X-RAY DIFFRACTIONf_chiral_restr0.04454673
X-RAY DIFFRACTIONf_plane_restr0.0075142
X-RAY DIFFRACTIONf_dihedral_angle_d12.690310766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.2513250.2258432X-RAY DIFFRACTION4.1
1.79-1.810.326300.236763X-RAY DIFFRACTION7.1
1.81-1.830.3044520.23641172X-RAY DIFFRACTION11.02
1.83-1.850.3029940.23741860X-RAY DIFFRACTION17.39
1.85-1.880.28491220.24082671X-RAY DIFFRACTION24.98
1.88-1.90.27371870.23733217X-RAY DIFFRACTION30.31
1.9-1.930.27552000.24743754X-RAY DIFFRACTION35.43
1.93-1.960.26442610.22964635X-RAY DIFFRACTION43.68
1.96-1.990.28872990.21935328X-RAY DIFFRACTION50.25
1.99-2.020.25483260.21655959X-RAY DIFFRACTION56.15
2.02-2.060.27093640.21776606X-RAY DIFFRACTION62.4
2.06-2.090.264140.20967072X-RAY DIFFRACTION66.9
2.09-2.130.25993670.20937664X-RAY DIFFRACTION71.87
2.13-2.180.24954470.20528016X-RAY DIFFRACTION75.7
2.18-2.220.2474330.20298454X-RAY DIFFRACTION79.28
2.22-2.280.25624160.19998861X-RAY DIFFRACTION82.8
2.28-2.330.25194410.19518611X-RAY DIFFRACTION80.87
2.33-2.40.25665120.19419678X-RAY DIFFRACTION91.23
2.4-2.470.24525050.19049948X-RAY DIFFRACTION93.46
2.47-2.550.25515100.182910024X-RAY DIFFRACTION94.05
2.55-2.640.24785090.189710046X-RAY DIFFRACTION94.36
2.64-2.740.24635270.189410063X-RAY DIFFRACTION94.68
2.74-2.870.22124980.191110025X-RAY DIFFRACTION93.65
2.87-3.020.24195230.18569371X-RAY DIFFRACTION88.58
3.02-3.210.21744990.171510109X-RAY DIFFRACTION94.65
3.21-3.450.21315230.16110165X-RAY DIFFRACTION95.76
3.45-3.80.1865410.140610099X-RAY DIFFRACTION94.81
3.8-4.350.16695180.13189658X-RAY DIFFRACTION91.04
4.35-5.480.17625160.13219815X-RAY DIFFRACTION92.19
5.48-44.220.17635310.17379772X-RAY DIFFRACTION92.2
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)
10.09339961300730.0639601545521-0.03206327551120.119048870553-0.03035836445380.0605047945264-0.04414439310110.04508532233310.0176293210158-0.05991315015580.0540157057740.0371762771489-0.03394528863470.006795961735330.00623781103550.163006833358-0.0224487295119-0.03131949658560.162218445256-0.001223313503010.0732681395616-15.4072905184-9.6116356361-50.8073218579
20.08551407505080.00129305161198-0.002054049501690.0325125116558-0.01530686448890.0614368322301-0.004835042947560.07192525076750.00545621037002-0.01569768366840.01621572315150.00559468274635-0.01040819242470.04289830661420.001941139546950.0868426590567-0.00966407512883-0.003602676322940.127482616848-0.0105478769860.05090741645249.62551234419-29.2977353547-34.3133841393
30.11028199660.0337143879902-0.02390966148540.077662260628-0.01434628709950.04119488784690.000662582727364-0.01339815559570.00773893667112-0.000143284357705-0.00336272717280.0178956788571-0.00876559102592-0.01850556828113.58252570682E-70.0832732634551-0.0004312416672310.0007824024456770.0777887666948-0.01500564657160.0781090241481-31.9057031677-20.8095080276-8.58913397644
40.08912448963440.0492634171987-0.02388078035490.0540152322507-0.03009225509340.04412833765-0.002958877810370.014975208609-0.0282856728727-0.0109694643982-0.00115406234534-0.007909306888480.0101450214167-0.00217741888149-2.776627303E-70.0907050701576-0.01330884666930.004847714248760.080027926814-0.03033917029290.108546614997-31.1607807991-50.8201842149-28.2450089653
50.08857403970660.0319655502694-0.0002726042977840.1109195415540.07806713453560.112861777834-0.0796854002084-0.154641595882-0.01680483010480.0729020201604-0.02201886412360.04469569016810.03272794579750.0737166690108-0.2102254293180.1258559544650.07537318679680.06806208330040.1994080448390.186438392030.0534309500836-4.38984667838-86.4267379342-57.1533459094
60.0948134256141-0.01807253656180.00150833788292-0.0003544527944290.01083873655280.04659942914490.0177585158794-0.124363476062-0.134135360296-0.02650423655290.009372504394390.0769566438681-0.03261877103650.01633620608380.02740720815840.0756044315461-0.00249086853186-0.001892920915570.1109946051030.04462957490590.211737513218-29.5898604708-78.2688604554-81.5175613742
70.09927594988710.0237583053267-0.006728194951740.0757386490582-0.01842576468130.0675957591472-0.0145698941728-0.0458688327506-0.00774793185450.007502368481070.0123982784189-0.00693461031419-0.03087428846860.0158233561193-2.69435186915E-70.0901449492625-0.01221695859680.005088358618460.103412832773-0.01469333940780.074527389913212.0405382025-51.1383678172-82.4741869791
80.0933471622253-0.00378935817789-0.02056711500970.0327131722174-0.0280399170370.04794422117840.0200067618432-0.00443018297504-0.0322055738416-0.0196537916545-0.01252119498040.01106748159170.00602956866430.00026922486480.007040719155180.09799322637030.01089242556040.0007482830908370.067396061578-0.01232445491480.11260699675611.0245331778-79.8745321107-103.86255903
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 2 through 475)AA2 - 4751 - 474
22(chain 'B' and resid 2 through 475)BB2 - 4751 - 474
33(chain 'C' and resid 1 through 475)CC1 - 4751 - 475
44(chain 'D' and resid 1 through 475)DD1 - 4751 - 475
55(chain 'E' and resid 2 through 475)EE2 - 4751 - 474
66(chain 'F' and resid 2 through 475)FF2 - 4751 - 474
77(chain 'G' and resid 1 through 475)GG1 - 4751 - 475
88(chain 'H' and resid 1 through 475)HH1 - 4751 - 475

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