2BVE

STRUCTURE OF THE N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH 2-PHENYL-PROP5AC

> Summary

Summary for 2BVE

Related1OD7 1OD9 1ODA 1QFO 1QFP 1URL
DescriptorSIALOADHESIN
Functional Keywordsimmune system, immunoglobulin, lectin, superfamily, carbohydrate binding, siglec, inhibitor design, cell adhesion
Biological sourceMUS MUSCULUS (MOUSE)
Cellular locationIsoform 1: Cell membrane; Single-pass type I membrane protein. Isoform 2: Secreted. Isoform 3: Secreted Q62230
Total number of polymer chains2
Total molecular weight27465.27
Authors
Zaccai, N.R.,May, A.P.,Robinson, R.C.,Burtnick, L.D.,Crocker, P.,Brossmer, R.,Kelm, S.,Jones, E.Y. (deposition date: 2005-06-27, release date: 2006-07-19, modification date: 2009-06-02)
Primary citation
Zaccai, N.R.,May, A.P.,Robinson, R.C.,Burtnick, L.D.,Crocker, P.,Brossmer, R.,Kelm, S.,Jones, E.Y.
Crystallographic and in Silico Analysis of the Sialoside-Binding Characteristics of the Siglec Sialoadhesin.
J.Mol.Biol., 365:1469-1479, 2007
PubMed: 17137591
DOI: 10.1016/j.jmb.2006.10.084
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.2 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers130.4%6.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 2bve
no rotation
Molmil generated image of 2bve
rotated about x axis by 90°
Molmil generated image of 2bve
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 2bve
no rotation
Molmil generated image of 2bve
rotated about x axis by 90°
Molmil generated image of 2bve
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (2bve.pdb1.gz [22.45 KB])
Coordinate files for Biological unit (2bve.pdb2.gz [22.74 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BSIALOADHESINpolymer11913319.22
UniProt (Q62230)
Pfam (PF07686)
MUS MUSCULUS (MOUSE)@PDBjSND1, SIALIC ACID BINDING IG-LIKE LECTIN-1, SIGLEC-1
2-PHENYL-PROP5ACnon-polymer413.42
waterwater18.0114

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight26638.4
Non-Polymers*Number of molecules2
Total molecular weight826.8
All*Total molecular weight27465.3
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.2 Å)

Cell axes31.97470.961102.650
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits19.72 - 2.20
the highest resolution shell value2.340 - 2.200
R-factor0.201
R-work0.20100
the highest resolution shell value0.248
R-free0.27000
the highest resolution shell value0.336
RMSD bond length0.011
RMSD bond angle1.500

Data Collection Statistics

Resolution limits20.00 - 2.10
the highest resolution shell value -
Number of reflections13244
Rmerge_l_obs0.130
the highest resolution shell value0.340
Completeness92.0
Redundancy4.95
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
15.6

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005576cellular_componentextracellular region
A0016021cellular_componentintegral component of membrane
A0005886cellular_componentplasma membrane
A0030246molecular_functioncarbohydrate binding
A0007155biological_processcell adhesion
A0006897biological_processendocytosis
A2001238biological_processpositive regulation of extrinsic apoptotic signaling pathway
A0070234biological_processpositive regulation of T cell apoptotic process
B0005576cellular_componentextracellular region
B0016021cellular_componentintegral component of membrane
B0005886cellular_componentplasma membrane
B0030246molecular_functioncarbohydrate binding
B0007155biological_processcell adhesion
B0006897biological_processendocytosis
B2001238biological_processpositive regulation of extrinsic apoptotic signaling pathway
B0070234biological_processpositive regulation of T cell apoptotic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC114BINDING SITE FOR RESIDUE PH5 A 1120
ChainResidue
ATRP2
AARG65
AARG97
ASER103
AARG105
ATRP106
ALEU107
AVAL109
AHOH
BTYR44
BARG48
BLEU107
BPH5
BHOH

AC213BINDING SITE FOR RESIDUE PH5 B 1119
ChainResidue
ATYR44
AARG48
AARG65
ALEU107
APH5
BTRP2
BARG97
BSER103
BARG105
BLEU107
BVAL109
BHOH
BHOH

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
PH5_2bve_A_112092-PHENYL-PROP5AC binding site
ChainResidueligand
ATRP2PH5: 2-PHENYL-PROP5AC
AARG97PH5: 2-PHENYL-PROP5AC
ASER103-VAL109PH5: 2-PHENYL-PROP5AC

PH5_2bve_B_111992-PHENYL-PROP5AC binding site
ChainResidueligand
BTRP2PH5: 2-PHENYL-PROP5AC
BARG97PH5: 2-PHENYL-PROP5AC
BSER103-VAL109PH5: 2-PHENYL-PROP5AC

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI12Sialic acid.
ChainResidueDetails
ATYR44
AARG97

SWS_FT_FI32Sialic acid.
ChainResidueDetails
BTYR44
BARG97

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb2bve.ent.gz (47.4 KB)
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all (no-compress)pdb2bve.ent (201 KB)
header onlypdb2bve.ent.gz (6.08 KB)
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PDBx/mmCIF2bve.cif.gz (59.29 KB)
PDBMLall2bve.xml.gz (89.43 KB)
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no-atom2bve-noatom.xml.gz (17.81 KB)
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ext-atom2bve-extatom.xml.gz (48.53 KB)
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PDBMLplusall2bve-plus.xml.gz (91.27 KB)
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no-atom2bve-plus-noatom.xml.gz (19.65 KB)
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add only2bve-add.xml.gz (1.84 KB)
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RDF2bve.rdf.gz (32.65 KB)
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Biological unit (PDB format)2bve.pdb1.gz (22.45 KB) (A)
*author and software defined assembly, 1 molecule(s) (monomeric)
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2bve.pdb2.gz (22.74 KB) (B)
*author and software defined assembly, 1 molecule(s) (monomeric)
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Validation reportsPDF2bve​_validation.pdf.gz (233.8 KB)
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PDF-full2bve​_full​_validation.pdf.gz (242.54 KB)
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XML2bve​_validation.xml.gz (7.93 KB)
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PNG2bve​_multipercentile​_validation.png.gz (119.79 KB)
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SVG2bve​_multipercentile​_validation.svg.gz (814 B)
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Sequence (fasta)2bve​_seq.txt
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