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- PDB-4c16: E-selectin lectin, EGF-like and two SCR domains complexed with gl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c16 | ||||||
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Title | E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic antagonist | ||||||
![]() | E-SELECTIN | ||||||
![]() | CELL ADHESION / CELL-ADHESION MOLECULE / C-TYPE LECTIN / INFLAMMATION / LEUKOCYTE / GLYCOMIMETIC / ANTAGONIST / CATCH- BOND | ||||||
Function / homology | ![]() actin filament-based process / positive regulation of leukocyte tethering or rolling / sialic acid binding / oligosaccharide binding / leukocyte migration involved in inflammatory response / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cortical cytoskeleton ...actin filament-based process / positive regulation of leukocyte tethering or rolling / sialic acid binding / oligosaccharide binding / leukocyte migration involved in inflammatory response / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cortical cytoskeleton / phospholipase binding / positive regulation of receptor internalization / : / response to tumor necrosis factor / clathrin-coated pit / response to interleukin-1 / response to cytokine / caveola / calcium-mediated signaling / Cell surface interactions at the vascular wall / transmembrane signaling receptor activity / regulation of inflammatory response / response to lipopolysaccharide / inflammatory response / membrane raft / external side of plasma membrane / perinuclear region of cytoplasm / extracellular space / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Preston, R.C. / Jakob, R.P. / Binder, F.P.C. / Sager, C.P. / Ernst, B. / Maier, T. | ||||||
![]() | ![]() Title: E-Selectin Ligand Complexes Adopt an Extended High-Affinity Conformation. Authors: Preston, R.C. / Jakob, R.P. / Binder, F.P. / Sager, C.P. / Ernst, B. / Maier, T. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.4 KB | Display | ![]() |
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PDB format | ![]() | 115.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 529.6 KB | Display | ![]() |
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Full document | ![]() | 537.7 KB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4csyC ![]() 1g1sS ![]() 1h04S ![]() 3govS ![]() 4c17 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.008697, -0.001289), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31305.760 Da / Num. of mol.: 2 Fragment: LECTIN DOMAIN, EGF-LIKE DOMAIN, SHORT CONSENSUS REPEAT DOMAIN 1, SHORT CONSENSUS REPEAT DOMAIN 2, RESDIUES 22-301 Source method: isolated from a genetically manipulated source Details: N-ACETYLGLUCOSAMINE RESIDUES ATTACHED TO ASN4, ASN124, ASN139, ASN158, ASN178, ASN182, AND ASN244 ON BOTH CHAINS. Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 18 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/FUC.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/FUC.gif)
#2: Sugar | ChemComp-NAG / #5: Sugar | #7: Sugar | |
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-Non-polymers , 4 types, 531 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/4WC.gif)
![](data/chem/img/Q6Z.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4WC.gif)
![](data/chem/img/Q6Z.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #6: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | {(1R,2R, 3S)-2-[(ALPHA-L-FUCOPYRANOSYL)OXY]-3-METHYL-CYCLOHEX-1-YL} 3-O- [SODIUM (1S)-1-CARBOXY-2- ...{(1R,2R, 3S)-2-[(ALPHA-L-FUCOPYRANO |
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Sequence details | WITHOUT N-TERMINAL SECRETION SIGNAL (AA. 1-21). SEQUENCE OF MATURE PROTEIN STARTS WITH RESIDUE 1 ...WITHOUT N-TERMINAL SECRETION SIGNAL (AA. 1-21). SEQUENCE OF MATURE PROTEIN STARTS WITH RESIDUE 1 FOR COMPATIBIL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.36 % / Description: NONE |
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Crystal grow | Details: PEG8000, HEPES, MOPS PH 6.2, CACL2, ANTAGONIST |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→57.43 Å / Num. obs: 50213 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 33.92 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2 / % possible all: 90.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1G1S,3GOV,1H04 Resolution: 1.93→15.81 Å / Cor.coef. Fo:Fc: 0.9325 / Cor.coef. Fo:Fc free: 0.9005 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.156
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Displacement parameters | Biso mean: 41.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.248 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→15.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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