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- PDB-31ao: A. niger ManA in covalent complex with pseudotrisaccharide inhibitor -

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Basic information

Entry
Database: PDB / ID: 31ao
TitleA. niger ManA in covalent complex with pseudotrisaccharide inhibitor
ComponentsProbable mannan endo-1,4-beta-mannosidase A
KeywordsHYDROLASE / Mannosidase
Function / homology
Function and homology information


mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / extracellular region
Similarity search - Function
GH family 5 beta-mannosidase-like / Mannan endo-1,4-beta-mannosidase-like / Glycoside hydrolase, family 5 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-YLL / Probable mannan endo-1,4-beta-mannosidase A
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.419 Å
AuthorsGote, T.A. / Armstrong, Z. / Tedeschi, M. / Lit, V.A.J. / Ram, A.F.J. / Davies, G.J. / Overkleeft, H.S.
Funding supportEuropean Union, Netherlands, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2020-SyG-951231European Union
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Chem Sci / Year: 2026
Title: The development of activity-based mannanase probes.
Authors: Tedeschi, M. / Lit, V.A.J. / McGregor, N.G.S. / Gote, T. / Kooloth Valappil, P. / Arentshorst, M. / Florea, B.I. / Gagestein, B. / Armstrong, Z. / Codee, J.D.C. / Nin-Hill, A. / Rovira, C. / ...Authors: Tedeschi, M. / Lit, V.A.J. / McGregor, N.G.S. / Gote, T. / Kooloth Valappil, P. / Arentshorst, M. / Florea, B.I. / Gagestein, B. / Armstrong, Z. / Codee, J.D.C. / Nin-Hill, A. / Rovira, C. / Ram, A.F.J. / Davies, G.J. / Overkleeft, H.S.
History
DepositionMay 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable mannan endo-1,4-beta-mannosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,37412
Polymers37,6451
Non-polymers1,72911
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-54 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.04, 68.226, 73.32
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable mannan endo-1,4-beta-mannosidase A / Endo-beta-1 / 4-mannanase A


Mass: 37645.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: manA, man1, An05g01320 / Production host: Aspergillus niger (mold)
References: UniProt: A2QKT4, mannan endo-1,4-beta-mannosidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 317 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-YLL / (1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL


Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.8 2.2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 2, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.419→30.95 Å / Num. obs: 64027 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.988 / Net I/σ(I): 4.6
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 6 % / Num. unique obs: 3093 / CC1/2: 0.209

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.128)refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.419→30.948 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.615 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2009 3126 4.882 %
Rwork0.1802 60901 -
all0.181 --
obs-64027 99.777 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.553 Å2-0 Å20 Å2
2---0.419 Å2-0 Å2
3----0.134 Å2
Refinement stepCycle: LAST / Resolution: 1.419→30.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 102 308 3063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122873
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162424
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.7733937
X-RAY DIFFRACTIONr_angle_other_deg0.6081.7345618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1545358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.63955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0210408
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.22410127
X-RAY DIFFRACTIONr_chiral_restr0.0870.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
X-RAY DIFFRACTIONr_nbd_refined0.2170.2538
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22259
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21467
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.215
X-RAY DIFFRACTIONr_nbd_other0.2490.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.229
X-RAY DIFFRACTIONr_mcbond_it1.2741.1011408
X-RAY DIFFRACTIONr_mcbond_other1.2741.1031409
X-RAY DIFFRACTIONr_mcangle_it1.9851.9741768
X-RAY DIFFRACTIONr_mcangle_other1.9861.9761769
X-RAY DIFFRACTIONr_scbond_it2.341.3661465
X-RAY DIFFRACTIONr_scbond_other2.0441.2631434
X-RAY DIFFRACTIONr_scangle_it3.5332.4212167
X-RAY DIFFRACTIONr_scangle_other3.1122.2412120
X-RAY DIFFRACTIONr_lrange_it4.98414.7743387
X-RAY DIFFRACTIONr_lrange_other4.70113.3473301
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
1.419-1.4560.3282120.32344160.32346770.90.90898.95230.328
1.456-1.4960.3082160.29343320.29445600.9270.93199.73680.298
1.496-1.5390.2832010.28342060.28344120.9380.93899.88670.287
1.539-1.5870.2922360.26940930.2743340.9390.94699.88460.273
1.587-1.6380.2552280.25239500.25241790.950.95499.97610.256
1.638-1.6960.2441700.2338150.23140250.9580.96199.00620.231
1.696-1.760.2341870.21937310.2239360.9630.96699.54270.22
1.76-1.8310.2232010.235800.20137810.9670.9731000.197
1.831-1.9120.2051690.1734540.17136230.9740.9811000.163
1.912-2.0050.2021440.16433300.16534740.9730.9841000.157
2.005-2.1130.1681330.1631870.1633200.9810.9851000.152
2.113-2.2410.1961520.1529750.15231270.9740.9871000.143
2.241-2.3950.1721260.13828370.13929630.980.9891000.13
2.395-2.5850.1581460.13426180.13527650.9840.98999.96380.127
2.585-2.830.171340.1424220.14225560.9840.9881000.133
2.83-3.1610.2011260.15621910.15823170.9770.9851000.152
3.161-3.6430.164710.14120040.14220750.9840.9881000.139
3.643-4.4470.131510.12316170.12317680.9910.9921000.125
4.447-6.2250.16550.16113640.16114190.9890.9891000.162
6.225-30.9480.246680.217790.2138500.9720.97899.64710.214

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