- PDB-3cd4: REFINEMENT AND ANALYSIS OF THE FIRST TWO DOMAINS OF HUMAN CD4 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3cd4
Title
REFINEMENT AND ANALYSIS OF THE FIRST TWO DOMAINS OF HUMAN CD4
Components
T CELL SURFACE GLYCOPROTEIN CD4
Keywords
T-CELL SURFACE GLYCOPROTEIN
Function / homology
Function and homology information
helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / response to methamphetamine hydrochloride / cellular response to ionomycin / T cell selection / MHC class II protein binding / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / response to methamphetamine hydrochloride / cellular response to ionomycin / T cell selection / MHC class II protein binding / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / response to vitamin D / regulation of T cell activation / extracellular matrix structural constituent / Other interleukin signaling / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of calcium ion transport into cytosol / regulation of calcium ion transport / positive regulation of protein kinase activity / Generation of second messenger molecules / macrophage differentiation / T cell differentiation / immunoglobulin binding / Co-inhibition by PD-1 / Binding and entry of HIV virion / coreceptor activity / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / positive regulation of protein phosphorylation / Cargo recognition for clathrin-mediated endocytosis / response to estradiol / signaling receptor activity / Clathrin-mediated endocytosis / virus receptor activity / defense response to Gram-negative bacterium / response to ethanol / adaptive immune response / positive regulation of viral entry into host cell / early endosome / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell adhesion / positive regulation of MAPK cascade / immune response / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / external side of plasma membrane / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function
SHEET RESIDUES 89 - 102 FORM ONE UNINTERRUPTED STRAND PASSING FROM DOMAIN 1 TO DOMAIN 2. RESIDUES ...SHEET RESIDUES 89 - 102 FORM ONE UNINTERRUPTED STRAND PASSING FROM DOMAIN 1 TO DOMAIN 2. RESIDUES 89 - 98 FORM STRAND 2 OF SHEET *S1* AND RESIDUES 99 - 103 FORM STRAND 1 OF SHEET *S4*.
Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modification
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
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Processing
Software
Name
Classification
X-PLOR
modelbuilding
X-PLOR
refinement
X-PLOR
phasing
Refinement
Rfactor Rwork: 0.197 / Rfactor obs: 0.197 / Highest resolution: 2.2 Å Details: THE SIDE CHAINS OF RESIDUES 72 AND 73 HAVE BEEN INCLUDED IN TWO ALTERNATE CONFORMATIONS AND THE SIDE CHAIN OF RESIDUE 43 HAS BEEN INCLUDED AT 0.5 OCCUPANCY. THE ELECTRON DENSITY SUGGESTS ...Details: THE SIDE CHAINS OF RESIDUES 72 AND 73 HAVE BEEN INCLUDED IN TWO ALTERNATE CONFORMATIONS AND THE SIDE CHAIN OF RESIDUE 43 HAS BEEN INCLUDED AT 0.5 OCCUPANCY. THE ELECTRON DENSITY SUGGESTS THAT RESIDUE 43 MAY HAVE MORE THAN TWO ALTERNATE CONFORMATIONS. IN THE ELECTRON DENSITY MAP RESIDUES 20 - 23, 105 - 107 AND 132 - 137 APPEAR DISORDERED AND THEIR POSITIONS ARE UNRELIABLE. FOR RESIDUES 1, 40, 43, 87, 88, 89, AND 152 SIDE CHAIN POSITIONS ARE SOMEWHAT UNCERTAIN AS INDICATED BY LARGE B VALUES.
Refinement step
Cycle: LAST / Highest resolution: 2.2 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1390
0
0
30
1420
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.015
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
2.42
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
X-RAY DIFFRACTION
x_mcangle_it
X-RAY DIFFRACTION
x_scbond_it
X-RAY DIFFRACTION
x_scangle_it
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