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- PDB-1tvx: NEUTROPHIL ACTIVATING PEPTIDE-2 VARIANT FORM M6L WITH FIVE ADDITI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tvx | ||||||
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Title | NEUTROPHIL ACTIVATING PEPTIDE-2 VARIANT FORM M6L WITH FIVE ADDITIONAL AMINO TERMINAL RESIDUES (DSDLY) | ||||||
![]() | NEUTROPHIL ACTIVATING PEPTIDE 2 VARIANT | ||||||
![]() | CYTOKINE | ||||||
Function / homology | ![]() glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity ...glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / Platelet degranulation / G alpha (i) signalling events / cellular response to lipopolysaccharide / defense response to bacterium / inflammatory response / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Malkowski, M.G. / Edwards, B.F.P. | ||||||
![]() | ![]() Title: The amino-terminal residues in the crystal structure of connective tissue activating peptide-III (des10) block the ELR chemotactic sequence. Authors: Malkowski, M.G. / Lazar, J.B. / Johnson, P.H. / Edwards, B.F. #1: ![]() Title: The Crystal Structure of Recombinant Human Neutrophil-Activating Peptide-2 (M6L) at 1.9-A Resolution Authors: Malkowski, M.G. / Wu, J.Y. / Lazar, J.B. / Johnson, P.H. / Edwards, B.F. #2: ![]() Title: Crystal Structure of Interleukin 8: Symbiosis of NMR and Crystallography Authors: Baldwin, E.T. / Weber, I.T. / Charles, R.St. / Xuan, J.C. / Appella, E. / Yamada, M. / Matsushima, K. / Edwards, B.F. / Clore, G.M. / Gronenborn, A.M. / al., et #3: ![]() Title: The Three-Dimensional Structure of Bovine Platelet Factor 4 at 3.0-A Resolution Authors: Charles, R.St. / Walz, D.A. / Edwards, B.F. | ||||||
History |
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Remark 700 | SHEET THERE IS A TETRAMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR IDENTICAL ...SHEET THERE IS A TETRAMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR IDENTICAL MONOMERS. TWO MONOMERS COMBINE TO FORM AN EXTENDED SIX STRANDED BETA SHEET DIMER. TWO DIMERS ARE THEN ARRANGED BACK-TO-BACK TO FORM THE TETRAMER. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.8 KB | Display | ![]() |
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PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.2 KB | Display | ![]() |
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Full document | ![]() | 446 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1napS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8217.521 Da / Num. of mol.: 4 Mutation: M26L AND A FIVE RESIDUE (DSDLY) INSERT AT THE AMINO TERMINUS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | THE NUMBERING SCHEME FOR ASP-CTAP FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE ...THE NUMBERING SCHEME FOR ASP-CTAP FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE RESIDUES IN BOVINE PLATELET FACTOR FOUR. THE NUMBERING SCHEME IS SEQUENTIAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 1.6M CITRATE, 0.1M HEPES, PH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→9.6 Å / Num. obs: 25385 / % possible obs: 88 % / Observed criterion σ(I): 1 / Rsym value: 0.0388 |
Reflection | *PLUS Num. measured all: 50642 / Rmerge(I) obs: 0.039 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NEUTROPHIL ACTIVATING PEPTIDE-2 (1NAP) Resolution: 1.75→7 Å
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Refinement step | Cycle: LAST / Resolution: 1.75→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 21058 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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