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- PDB-1lk3: ENGINEERED HUMAN INTERLEUKIN-10 MONOMER COMPLEXED TO 9D7 FAB FRAGMENT -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lk3 | ||||||
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Title | ENGINEERED HUMAN INTERLEUKIN-10 MONOMER COMPLEXED TO 9D7 FAB FRAGMENT | ||||||
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![]() | IMMUNE SYSTEM / ANTIGEN-ANTIBODY COMPLEX | ||||||
Function / homology | ![]() Classical antibody-mediated complement activation / FCGR activation / Regulation of Complement cascade / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / Role of phospholipids in phagocytosis / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation ...Classical antibody-mediated complement activation / FCGR activation / Regulation of Complement cascade / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / Role of phospholipids in phagocytosis / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / Initial triggering of complement / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / response to carbon monoxide / positive regulation of plasma cell differentiation / positive regulation of B cell apoptotic process / response to inactivity / Regulation of actin dynamics for phagocytic cup formation / chronic inflammatory response to antigenic stimulus / cytoplasmic sequestering of NF-kappaB / negative regulation of membrane protein ectodomain proteolysis / regulation of isotype switching / negative regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production involved in immune response / negative regulation of interleukin-1 production / positive regulation of B cell activation / negative regulation of MHC class II biosynthetic process / branching involved in labyrinthine layer morphogenesis / negative regulation of interleukin-8 production / negative regulation of nitric oxide biosynthetic process / phagocytosis, recognition / negative regulation of interleukin-12 production / type 2 immune response / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / endothelial cell apoptotic process / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / leukocyte chemotaxis / positive regulation of heterotypic cell-cell adhesion / positive regulation of signaling receptor activity / CD163 mediating an anti-inflammatory response / negative regulation of cytokine production / positive regulation of immunoglobulin production / cellular response to hepatocyte growth factor stimulus / phagocytosis, engulfment / regulation of synapse organization / positive regulation of sprouting angiogenesis / B cell proliferation / negative regulation of B cell proliferation / defense response to protozoan / negative regulation of vascular associated smooth muscle cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / hemopoiesis / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of mitotic cell cycle / positive regulation of cell cycle / negative regulation of T cell proliferation / response to glucocorticoid / immunoglobulin complex, circulating / positive regulation of vascular associated smooth muscle cell proliferation / immunoglobulin receptor binding / positive regulation of endothelial cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of autophagy / B cell differentiation / FCGR3A-mediated IL10 synthesis / response to activity / positive regulation of cytokine production / cytokine activity / complement activation, classical pathway / cellular response to estradiol stimulus / liver regeneration / antigen binding / B cell receptor signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to insulin / response to molecule of bacterial origin / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / regulation of gene expression / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / protein dimerization activity / defense response to bacterium / response to xenobiotic stimulus / negative regulation of cell population proliferation / external side of plasma membrane / innate immune response / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Josephson, K. / Jones, B.C. / Walter, L.J. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R. | ||||||
![]() | ![]() Title: Noncompetitive antibody neutralization of IL-10 revealed by protein engineering and x-ray crystallography. Authors: Josephson, K. / Jones, B.C. / Walter, L.J. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R. #1: ![]() Title: Design and Analysis of an Engineered Human Interleukin-10 Monomer Authors: Josephson, K. / DiGiacomo, R. / Indelicato, S.R. / Iyo, A.H. / Nagabhushan, T.L. / Parker, M.H. / Walter, M.R. / Ayo, A.H. | ||||||
History |
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Remark 999 | SEQUENCE USING BLAST NO APPROPRIATE SEQUENCE DATABASE MATCH WAS FOUND FOR 9D7 LIGHT CHAIN, CHAINS ...SEQUENCE USING BLAST NO APPROPRIATE SEQUENCE DATABASE MATCH WAS FOUND FOR 9D7 LIGHT CHAIN, CHAINS L,M AND 9D7 HEAVY CHAIN, CHAINS H,I. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.3 KB | Display | ![]() |
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PDB format | ![]() | 207.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473 KB | Display | ![]() |
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Full document | ![]() | 494.5 KB | Display | |
Data in XML | ![]() | 55 KB | Display | |
Data in CIF | ![]() | 82.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18520.324 Da / Num. of mol.: 2 / Fragment: Residues 26-175 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 22794.438 Da / Num. of mol.: 2 / Fragment: Fab fragment, Residues 1-210 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) ![]() ![]() #3: Antibody | Mass: 23529.443 Da / Num. of mol.: 2 / Fragment: Fab fragment, Residues 1-219 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: peg 4000, sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1999 |
Radiation | Monochromator: Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 96708 / Num. obs: 96708 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 23.11 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.91→1.95 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.34 / % possible all: 72.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 357669 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 72.6 % / Rmerge(I) obs: 0.34 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.91→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |