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- PDB-1url: N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH GLYCOPEPTIDE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1url | ||||||
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Title | N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH GLYCOPEPTIDE | ||||||
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![]() | SUGAR BINDING PROTEIN/IMMUNE SYSTEM / LECTIN/IG-DOMAIN / SIALOADHESIN / OLIGOSACCHARIDE MIMICS / MOLECULAR MIMICRY / CELL ADHESION / LECTIN / IMMUNOGLOBULIN DOMAIN / SUGAR BINDING PROTEIN IMMUNE SYSTEM COMPLEX / SUGAR BINDING PROTEIN / IMMUNE SYSTEM / SUGAR BINDING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() positive regulation of T cell apoptotic process / virion binding / positive regulation of extrinsic apoptotic signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / late endosome / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / early endosome / cell adhesion / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bukrinsky, J.T. / Hilaire, P.M.S. / Meldal, M. / Crocker, P.R. / Henriksen, A. | ||||||
![]() | ![]() Title: Complex of Sialoadhesin with a Glycopeptide Ligand Authors: Bukrinsky, J.T. / Hilaire, P.M.S. / Meldal, M. / Crocker, P.R. / Henriksen, A. #1: ![]() Title: Crystal Structure of the N-Terminal Domain of Sialoadhesin in Complex with 3' Sialyllactose at 1.85 A Resolution. Authors: May, A.P. / Robinson, R.C. / Vinson, M. / Crocker, P.R. / Jones, E.Y. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.3 KB | Display | ![]() |
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PDB format | ![]() | 26.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qfoS S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Details | THE ENTRY IS MARKED AS DIMERIC AS PEPTIDE CHAIN B IS IN COMPLEX WITH PROTEIN CHAIN A FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350. |
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Components
#1: Protein | Mass: 13204.021 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 20-137 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 764.812 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: HIA IS A MODIFIED HISTIDINE, O-SIALIC ACID BOUND ON THR B 4 Source: (synth.) synthetic construct (others) |
#3: Sugar | ChemComp-SIA / |
#4: Water | ChemComp-HOH / |
Compound details | MOL_ID 1 IS MACROPHAGE-RESTRICTED ADHESION MOLECULE THAT MEDIATES SIALIC-ACID DEPENDENT BINDING TO ...MOL_ID 1 IS MACROPHAGE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.6 % |
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Crystal grow | pH: 5.6 / Details: 30% PEG4000, 0.1 M NA-CITRATE, 0.2 M AMSO4 PH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.192 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→28.7 Å / Num. obs: 4194 / % possible obs: 87.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.4→2.52 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.6 / % possible all: 73.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QFO Resolution: 2.4→28.74 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 659043.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: CYS A 17 MAKES A DISULPHIDE BOND WITH A SYMMETRY RELATED MOLECULE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.2074 Å2 / ksol: 0.366536 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→28.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
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Xplor file |
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