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- PDB-9rav: Streptococcus pyogenes GapN in complex with 4-hydroxypyridazine -

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Basic information

Entry
Database: PDB / ID: 9rav
TitleStreptococcus pyogenes GapN in complex with 4-hydroxypyridazine
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
: / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWirsing, R. / Schindelin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Streptococcus pyogenes GapN in complex with 4-hydroxypyridazine (R76)
Authors: Wirsing, R. / Schindelin, H.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 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)425,96732
Polymers423,6738
Non-polymers2,29424
Water80,3834462
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)212,98516
Polymers211,8374
Non-polymers1,14912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18390 Å2
ΔGint-187 kcal/mol
Surface area58740 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)212,98216
Polymers211,8374
Non-polymers1,14512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18240 Å2
ΔGint-172 kcal/mol
Surface area59070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.574, 98.985, 103.231
Angle α, β, γ (deg.)77.680, 75.950, 67.510
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-A1JDY / 4-hydroxypyridazine / pyridazin-4-ol


Mass: 96.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H4N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4462 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.15 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.44→48.42 Å / Num. obs: 497136 / % possible obs: 50.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.036 / Net I/σ(I): 9.5
Reflection shellResolution: 1.44→1.69 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 49116 / CC1/2: 0.74

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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: 1.5→48.42 Å / SU ML: 0.1747 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.1812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2066 15488 5.04 %
Rwork0.1679 291860 -
obs0.1698 307348 55.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28360 0 139 4462 32961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007829346
X-RAY DIFFRACTIONf_angle_d0.705439887
X-RAY DIFFRACTIONf_chiral_restr0.0654691
X-RAY DIFFRACTIONf_plane_restr0.00675170
X-RAY DIFFRACTIONf_dihedral_angle_d12.083910727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.510.323220.2695339X-RAY DIFFRACTION1.97
1.51-1.530.4349290.2267455X-RAY DIFFRACTION2.67
1.53-1.550.3698310.2223634X-RAY DIFFRACTION3.62
1.55-1.570.2813400.2396766X-RAY DIFFRACTION4.39
1.57-1.590.2659600.23211062X-RAY DIFFRACTION6.14
1.59-1.610.2745740.23891460X-RAY DIFFRACTION8.32
1.61-1.640.2526820.25721901X-RAY DIFFRACTION10.78
1.64-1.660.23811160.24512294X-RAY DIFFRACTION13.07
1.66-1.690.27411810.23552794X-RAY DIFFRACTION16.13
1.69-1.710.2432120.24273747X-RAY DIFFRACTION21.5
1.71-1.740.26152720.22674794X-RAY DIFFRACTION27.55
1.74-1.780.2523160.22586081X-RAY DIFFRACTION34.75
1.78-1.810.244650.2167585X-RAY DIFFRACTION43.66
1.81-1.850.25685300.21039884X-RAY DIFFRACTION56.57
1.85-1.890.2676120.215311945X-RAY DIFFRACTION68.36
1.89-1.930.28047220.245213646X-RAY DIFFRACTION78.04
1.93-1.980.23677870.196815085X-RAY DIFFRACTION85.74
1.98-2.030.23518370.182715591X-RAY DIFFRACTION89.43
2.03-2.090.24898410.19615720X-RAY DIFFRACTION90.22
2.09-2.160.21759150.170615819X-RAY DIFFRACTION90.81
2.16-2.240.23578290.176615749X-RAY DIFFRACTION90.05
2.24-2.330.22859010.172815674X-RAY DIFFRACTION89.85
2.33-2.430.20798020.164515739X-RAY DIFFRACTION89.7
2.43-2.560.21448060.170815818X-RAY DIFFRACTION90.54
2.56-2.720.21598580.179216059X-RAY DIFFRACTION91.78
2.72-2.930.20678190.168116374X-RAY DIFFRACTION93.41
2.93-3.230.21598240.16316343X-RAY DIFFRACTION93.1
3.23-3.690.17898280.148116124X-RAY DIFFRACTION92.25
3.69-4.650.15598620.124315922X-RAY DIFFRACTION91.02
4.65-48.420.17148150.15416456X-RAY DIFFRACTION93.81
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)
10.1583212369290.05564626156680.0214631383320.1222708255980.03618064860480.3636876379890.007699565426750.04252077845070.0309964501707-0.056288065237-0.00432350558010.0049601622695-0.07429255530580.04168218751780.05678229954970.1052052833630.00177380332174-0.002843860895780.1081430517470.00637612427360.0607126062832-15.7306778763-8.74300311029-51.5104060166
20.178816483278-0.01152084737680.0737644343350.02840319875430.02545679453060.1312005290870.007733949556580.06741303354890.00802575567429-0.0143932211332-0.000355831059057-0.006261135778120.001359297861610.0454704713110.01638842588910.0758995528456-0.00723577232294-0.006288247303950.111757321243-0.001611545130560.07283455375539.04261834354-28.3938739265-35.1092794034
30.172144673574-0.046214841414-0.02599979746170.1166155530830.03365998731770.164733703855-0.0060615569095-0.006196952414150.01088005614740.0129167385149-0.001915329390760.027380019899-0.0223506442432-0.02143290025020.0003671012831410.0707334359298-0.01372331176480.005225390743710.0669556293092-0.004275907115510.0683598251396-32.0979770418-19.9839166123-9.53189574272
40.2190589536540.118106707658-0.007862842796840.1935641740590.00975469425030.111542890374-0.01001539892220.0254133014104-0.0248341005791-0.003643421209380.01464620939-0.003489764883830.0116154078253-0.006420762103850.006584606196020.0655840986007-0.01107772316310.002610159858680.0739553769502-0.01715935192790.0661239594962-31.1804005887-49.6451238591-28.8651776341
50.186328797803-0.11564487229-0.08197972514420.345873627842-0.0616711503720.379645072412-0.0622588417567-0.068541885676-0.04337487295820.1062690249180.03959435092560.04229337677850.05327266474160.0309668999589-0.05179378403190.1308689632690.0156842970650.01592477855020.09333736509280.02718835197270.0990232960251-4.19784617476-85.4588949065-57.8779341828
60.541800119792-0.1818279127580.01278361471030.08913212650580.04087055958320.0688533303926-0.0102432008913-0.10979763641-0.181737435883-0.005149138009310.02067119770890.09668911555990.00616898587563-0.01926109345050.01800976681590.0696064087367-0.007271685293940.008402861144380.07096277701540.04094913808750.16172289528-28.976391626-78.0560661967-82.2842013644
70.17354305290.02614113838840.04746950096010.190494986902-0.01841465503720.0989152339917-0.0124052767173-0.02241277623280.005501124062890.007650206025010.00508593376471-0.0065361931507-0.02068757214060.00809954510981-0.002061616029150.072368326427-0.007384961186450.009497029123290.0621165232728-0.005235795467920.06347439349812.1235826173-50.5660249141-83.4409458943
80.208150401631-0.0606150457291-0.06934614894290.07606134175770.005878221117860.195167191114-0.0008337448577860.00236853331245-0.0283619930364-0.0159224168003-0.008525883225040.01806368132720.02454498985130.00808607059079-0.007991791946120.07524388886610.001508326436360.002632986669310.0407606754581-0.002279107256830.092284330362311.4128986299-79.7795579754-104.47914295
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)BE2 - 4751 - 474
33(chain 'C' and resid 2 through 475)CH2 - 4751 - 474
44(chain 'D' and resid 1 through 475)DL1 - 4751 - 475
55(chain 'E' and resid 2 through 475)EQ2 - 4751 - 474
66(chain 'F' and resid 2 through 475)FT2 - 4751 - 474
77(chain 'G' and resid 1 through 475)GW1 - 4751 - 475
88(chain 'H' and resid 1 through 475)HAA1 - 4751 - 475

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