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- PDB-5in4: Crystal Structure of GDP-mannose 4,6 dehydratase bound to a GDP-f... -

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Basic information

Entry
Database: PDB / ID: 5in4
TitleCrystal Structure of GDP-mannose 4,6 dehydratase bound to a GDP-fucose based inhibitor
ComponentsGDP-mannose 4,6 dehydratase
KeywordsLYASE/INHIBITOR / GDP-mannose 4 / 6 dehydratase / antibody fucosylation / LYASE-INHIBITOR complex
Function / homology
Function and homology information


GDP-L-fucose biosynthetic process / GDP-fucose biosynthesis / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / Notch signaling pathway / extracellular exosome / identical protein binding ...GDP-L-fucose biosynthetic process / GDP-fucose biosynthesis / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / Notch signaling pathway / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
GDP-mannose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6CK / GUANOSINE-5'-DIPHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-mannose 4,6 dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsSickmier, E.A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with GDP-Mannose 4,6-Dehydratase.
Authors: Allen, J.G. / Mujacic, M. / Frohn, M.J. / Pickrell, A.J. / Kodama, P. / Bagal, D. / San Miguel, T. / Sickmier, E.A. / Osgood, S. / Swietlow, A. / Li, V. / Jordan, J.B. / Kim, K.W. / ...Authors: Allen, J.G. / Mujacic, M. / Frohn, M.J. / Pickrell, A.J. / Kodama, P. / Bagal, D. / San Miguel, T. / Sickmier, E.A. / Osgood, S. / Swietlow, A. / Li, V. / Jordan, J.B. / Kim, K.W. / Rousseau, A.C. / Kim, Y.J. / Caille, S. / Achmatowicz, M. / Thiel, O. / Fotsch, C.H. / Reddy, P. / McCarter, J.D.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-mannose 4,6 dehydratase
B: GDP-mannose 4,6 dehydratase
C: GDP-mannose 4,6 dehydratase
D: GDP-mannose 4,6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,92016
Polymers166,6014
Non-polymers7,32012
Water25,5811420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22450 Å2
ΔGint-85 kcal/mol
Surface area45760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.028, 140.077, 85.953
Angle α, β, γ (deg.)90.000, 106.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GDP-mannose 4,6 dehydratase / GDP-D-mannose dehydratase / GMD


Mass: 41650.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMDS / Production host: Enterobacteria phage L1 (virus) / References: UniProt: O60547, GDP-mannose 4,6-dehydratase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-6CK / [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(trifluoromethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)


Mass: 643.313 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H22F3N5O15P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1420 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium fluoride and 20% PEG 3350. The crystals were briefly transferred to a cryoprotectant consisting of 0.2 M potassium fluoride, 20% PEG 3350, and 20% glycerol and flash frozen in liquid nitrogen

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 184649 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Χ2: 0.825 / Net I/av σ(I): 14.367 / Net I/σ(I): 10.6 / Num. measured all: 600654
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.662.60.525189.9
1.66-1.722.90.518197
1.72-1.83.20.442199.9
1.8-1.93.30.3161100
1.9-2.023.30.1941100
2.02-2.173.40.125199.9
2.17-2.393.40.089199.9
2.39-2.743.40.065199.9
2.74-3.453.40.049199.9
3.45-303.50.045199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2142refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.6→29.575 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.01
RfactorNum. reflection% reflection
Rfree0.1762 8630 4.97 %
Rwork0.1461 --
obs0.1476 173795 90.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.25 Å2 / Biso mean: 18.5988 Å2 / Biso min: 4.83 Å2
Refinement stepCycle: final / Resolution: 1.6→29.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11288 0 468 1420 13176
Biso mean--12.71 31.14 -
Num. residues----1408

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