[English] 日本語
Yorodumi
- PDB-5in4: Crystal Structure of GDP-mannose 4,6 dehydratase bound to a GDP-f... -

+
Open data


ID or keywords:

Loading...

-
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-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 / cytoplasm / cytosol
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more