- PDB-1wmg: Crystal structure of the UNC5H2 death domain -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1wmg
Title
Crystal structure of the UNC5H2 death domain
Components
netrin receptor Unc5h2
Keywords
APOPTOSIS / six helix bundle / death domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information
netrin receptor activity / anterior/posterior axon guidance / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / axon guidance / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / apoptotic process ...netrin receptor activity / anterior/posterior axon guidance / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / axon guidance / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / apoptotic process / plasma membrane / cytosol Similarity search - Function
UNC5B, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas / Death Domain, Fas ...UNC5B, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas / Death Domain, Fas / Thrombospondin type 1 domain / Death domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Resolution: 2.1→2.18 Å / Rsym value: 0.241 / % possible all: 99.2
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Processing
Software
Name
Version
Classification
CNS
1.1
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→39.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 824690.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: The structure was refined also with ARP/wARP. The file contains Friedel pairs.
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