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- PDB-2fyd: catalytic domain of bovine beta 1, 4-galactosyltransferase in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fyd | ||||||
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Title | catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with alpha-lactalbumin, glucose, Mn, and UDP-N-acetylgalactosamine | ||||||
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![]() | TRANSFERASE / lactose sythase / catalytic intermediate | ||||||
Function / homology | ![]() Lactose synthesis / protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase ...Lactose synthesis / protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity / positive regulation of circulating fibrinogen levels / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / UDP-galactosyltransferase activity / Golgi trans cisterna / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / alpha-tubulin binding / cytoskeletal protein binding / filopodium / brush border membrane / lipid metabolic process / lysozyme activity / manganese ion binding / basolateral plasma membrane / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / external side of plasma membrane / calcium ion binding / Golgi apparatus / protein-containing complex / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramakrishnan, B. / Ramasamy, V. / Qasba, P.K. | ||||||
![]() | ![]() Title: Structural Snapshots of beta-1,4-Galactosyltransferase-I Along the Kinetic Pathway. Authors: Ramakrishnan, B. / Ramasamy, V. / Qasba, P.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.9 KB | Display | ![]() |
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PDB format | ![]() | 146.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fy7C ![]() 2fyaC ![]() 2fybC ![]() 2fycC ![]() 1oqmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 14015.835 Da / Num. of mol.: 2 / Mutation: W312C, C342T, P401C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 32772.539 Da / Num. of mol.: 2 / Fragment: residues 57-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 21450879, UniProt: P08037*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/BGC.gif)
![](data/chem/img/NGA.gif)
![](data/chem/img/NGA.gif)
#6: Sugar | #7: Sugar | |
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-Non-polymers , 6 types, 519 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 50 mM Mes-NaOH, 6% PEG 4000, pH 6.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2004 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.08 Å / Num. obs: 68901 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.102 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 6650 / Rsym value: 0.568 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OQM Resolution: 2→32.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1608743.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Although intact UDP-GalNAc was used in the crystallization, in the crystal structure the GalNAc moiety is cleaved off from UDP-GalNAc. This cleaved off sugar exists without O1 oxygen atom ...Details: Although intact UDP-GalNAc was used in the crystallization, in the crystal structure the GalNAc moiety is cleaved off from UDP-GalNAc. This cleaved off sugar exists without O1 oxygen atom similar to an oxocarbenium ion or a N-acetylgalactal form, which cannot be distinguished at the present resolution
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.0191 Å2 / ksol: 0.337351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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