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- PDB-9swy: The structure of AfUAP1 in complex with GlcNAc-1P -

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Basic information

Entry
Database: PDB / ID: 9swy
TitleThe structure of AfUAP1 in complex with GlcNAc-1P
Components(UDP-N-acetylglucosamine diphosphorylase) x 2
KeywordsTRANSFERASE / UAP / GlcNAc-1P / conformation
Function / homologyUDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / Nucleotide-diphospho-sugar transferases / Chem-GN1 / UDP-N-acetylglucosamine diphosphorylase
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsYan, K. / Raimi, O. / Chen, X.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
CitationJournal: Febs Lett. / Year: 2026
Title: Cell wall target fragment discovery using a low-cost, minimal fragment library.
Authors: Yan, K. / Stanley, M. / Raimi, O. / Ferenbach, A.T. / Dorfmueller, H.C. / van Aalten, D.M.F.
History
DepositionOct 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: UDP-N-acetylglucosamine diphosphorylase
A: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0404
Polymers107,7032
Non-polymers3372
Water3,891216
1
B: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1812
Polymers53,8801
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8592
Polymers53,8231
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.834, 136.865, 143.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-acetylglucosamine diphosphorylase


Mass: 53880.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: KXV57_008857 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A229XUD0, UDP-N-acetylglucosamine diphosphorylase
#2: Protein UDP-N-acetylglucosamine diphosphorylase


Mass: 53823.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: KXV57_008857 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A229XUD0, UDP-N-acetylglucosamine diphosphorylase
#3: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 25% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.72→71.54 Å / Num. obs: 115021 / % possible obs: 98.2 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 4713 / CC1/2: 0.314

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→71.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.013 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25186 1925 1.7 %RANDOM
Rwork0.21044 ---
obs0.21112 110112 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.559 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å2-0 Å2-0 Å2
2---2.22 Å2-0 Å2
3----1.99 Å2
Refinement stepCycle: 1 / Resolution: 1.72→71.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 20 216 7580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166939
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.64710196
X-RAY DIFFRACTIONr_angle_other_deg0.4751.56416212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.219540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23101264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021434
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_it3.64.5173807
X-RAY DIFFRACTIONr_mcbond_other3.5994.5173807
X-RAY DIFFRACTIONr_mcangle_it4.9496.7574748
X-RAY DIFFRACTIONr_mcangle_other4.9486.7584749
X-RAY DIFFRACTIONr_scbond_it4.0994.7973727
X-RAY DIFFRACTIONr_scbond_other4.0994.7973728
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0847.0515446
X-RAY DIFFRACTIONr_long_range_B_refined7.65556.5838171
X-RAY DIFFRACTIONr_long_range_B_other7.63256.0318122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.524 94 -
Rwork0.517 4821 -
obs--57.34 %

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