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- PDB-1ilq: CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 (MINIMIZED MEAN) -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ilq | |||||||||
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Title | CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 (MINIMIZED MEAN) | |||||||||
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![]() | CYTOKINE | |||||||||
Function / homology | ![]() interleukin-8 receptor activity / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / interleukin-8 binding / positive regulation of cellular biosynthetic process / chemokine receptor activity / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress ...interleukin-8 receptor activity / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / interleukin-8 binding / positive regulation of cellular biosynthetic process / chemokine receptor activity / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress / CXCR chemokine receptor binding / embryonic digestive tract development / induction of positive chemotaxis / C-C chemokine receptor activity / C-C chemokine binding / neutrophil activation / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / neutrophil chemotaxis / secretory granule membrane / G protein-coupled receptor activity / calcium-mediated signaling / response to molecule of bacterial origin / receptor internalization / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of angiogenesis / chemotaxis / cellular response to tumor necrosis factor / heparin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cell surface receptor signaling pathway / intracellular signal transduction / inflammatory response / immune response / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / external side of plasma membrane / negative regulation of gene expression / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS | |||||||||
![]() | Skelton, N.J. / Quan, C. / Lowman, H. | |||||||||
![]() | ![]() Title: Structure of a CXC chemokine-receptor fragment in complex with interleukin-8. Authors: Skelton, N.J. / Quan, C. / Reilly, D. / Lowman, H. #1: ![]() Title: Peptide Based Inhibitors of Il-8: Structural Simplification and Improved Potency Authors: Attwood, M.R. / al., et #2: ![]() Title: Three-Dimensional Structure of Il-8 in Solution Authors: Clore, G.M. / Appella, E. / Yamada, M. / Gronenborn, A.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.1 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 353.9 KB | Display | ![]() |
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Full document | ![]() | 359.6 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 8401.807 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 2068.220 Da / Num. of mol.: 1 / Fragment: 9-29 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE ASSIGNMENTS WERE MADE USING TRIPLE RESONANCE NMR EXPERIMENTS CONDUCTED ON 13C/15N LABELED IL-8 BOUND TO UNLABELED CXCR-1 PEPTIDE (SEE JRNL ENTRY FOR MORE DETAILS) NOE RESTRAINTS WERE ...Text: THE ASSIGNMENTS WERE MADE USING TRIPLE RESONANCE NMR EXPERIMENTS CONDUCTED ON 13C/15N LABELED IL-8 BOUND TO UNLABELED CXCR-1 PEPTIDE (SEE JRNL ENTRY FOR MORE DETAILS) NOE RESTRAINTS WERE OBTAINED FROM 15N EDITED EXPERIMENTS (INTRA IL8), 13C OR 15N FILTERED EXPERIMENTS (INTRA CXCR-1) OR 13C-FILTERED/ EDITED EXPERIMENTS (INTERMOLECULAR RESTRAINTS) |
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Sample preparation
Sample conditions | Ionic strength: 0.15 M / pH: 5.50 / Pressure: 1 atm / Temperature: 308.00 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX 500 / Manufacturer: Bruker / Model: AMX 500 / Field strength: 500 MHz |
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Processing
Software | Name: ![]() | ||||||||||||
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NMR software |
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Refinement | Method: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 Details: INITIAL COORDINATES FOR IL-8 WERE TAKEN FROM PDB ENTRY 1IL8; A LINEAR CHAIN FOR THE CXCR-1 FRAGMENT WAS BUILT IN INSIGHT (MSI). THE CXCR-1 FRAGMENT WAS POSITIONED RANDOMLY WITH RESPECT TO ...Details: INITIAL COORDINATES FOR IL-8 WERE TAKEN FROM PDB ENTRY 1IL8; A LINEAR CHAIN FOR THE CXCR-1 FRAGMENT WAS BUILT IN INSIGHT (MSI). THE CXCR-1 FRAGMENT WAS POSITIONED RANDOMLY WITH RESPECT TO IL8 - OBTAIN 40 STARTING CONFORMATIONS. THE INITIAL STRUCTURES WERE THEN REFINED USING RMD WITH THE AMBER ALL ATOM FORCE FIELD AS IMPLIMENTED WITHIN DISCOVER. ALL OF IL8 MONOMER B AND PARTS OF IL8 MONOMER A (2-7, 22-38 AND 51-72) WERE KEPT FIXED DURING THE REFINEMENT SINCE CHEMICAL SHIFT CHANGES INDICATED THAT THESE PORTION OF THE MOLECULE WERE NOT PERTURBED BY PEPTIDE BINDING. THIS MODEL IS THE RESULT OF RESTRAINED ENERGY MINIMIZATION OF THE GEOMETRIC MEAN OF 20 STRUCTURES FROM THE ENSEMBLE (ENTRY 1ILP) SEE JRNL ENTRY FOR MORE DETAILS. | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION ENERGY Conformers calculated total number: 40 / Conformers submitted total number: 1 |