- PDB-6s8v: Structure of the high affinity Anticalin P3D11 in complex with th... -
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Basic information
Entry
Database: PDB / ID: 6s8v
Title
Structure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy chain ectodomain
Components
4F2 cell-surface antigen heavy chain
Neutrophil gelatinase-associated lipocalin
Keywords
PROTEIN BINDING / Lipocalin / Lcn2 / Anticalin / lipocalin-based binding protein / CD98hc / 4F2hc / amino acid transport / presentation of CD98 light chains / interaction with integrin beta subunits / single-pass type II membrane protein
Function / homology
Function and homology information
neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane ...neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / isoleucine transport / L-alanine import across plasma membrane / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / proline transport / siderophore transport / Metal sequestration by antimicrobial proteins / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / iron ion sequestering activity / enterobactin binding / anchoring junction / Basigin interactions / amino acid transport / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / Iron uptake and transport / specific granule lumen / calcium ion transport / double-stranded RNA binding / melanosome / virus receptor activity / positive regulation of cold-induced thermogenesis / basolateral plasma membrane / Interleukin-4 and Interleukin-13 signaling / carbohydrate metabolic process / defense response to bacterium / cadherin binding / symbiont entry into host cell / iron ion binding / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / innate immune response / apoptotic process / synapse / Neutrophil degranulation / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane Similarity search - Function
Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Calycin beta-barrel core domain ...Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Glycosyl hydrolase, all-beta / Calycin / Lipocalin / Lipocalin signature. / Glycoside hydrolase superfamily / Beta Barrel / Mainly Beta Similarity search - Domain/homology
Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.836 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.125 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2263
2234
2 %
RANDOM
Rwork
0.1845
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-
-
obs
0.1853
111018
99.86 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
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