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- PDB-1kjs: NMR SOLUTION STRUCTURE OF C5A AT PH 5.2, 303K, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1kjs
TitleNMR SOLUTION STRUCTURE OF C5A AT PH 5.2, 303K, 20 STRUCTURES
ComponentsC5A
KeywordsCELL ADHESION / AGGREGATION / CHEMOTAXIS / GP AGONIST / C5A RECEPTOR AGONIST
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin ...Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / AB INITIO SIMULATED ANNEALING
AuthorsZhang, X. / Boyar, W. / Toth, M. / Wennogle, L. / Gonnella, N.C.
CitationJournal: Proteins / Year: 1997
Title: Structural definition of the C5a C terminus by two-dimensional nuclear magnetic resonance spectroscopy.
Authors: Zhang, X. / Boyar, W. / Toth, M.J. / Wennogle, L. / Gonnella, N.C.
History
DepositionJan 9, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C5A


Theoretical massNumber of molelcules
Total (without water)8,3191
Polymers8,3191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500VIOLATIONS: NOE<0.5A, DIHE<5.0, BONDS<0.05A, ANGLES<5.0 IMPROPERS<5.0
Representative

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Components

#1: Protein C5A / COMPLEMENT C5A


Mass: 8318.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PB-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P01031
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121RELAYED-COSY
131TQ
141DQ
151TOCSY
161NOESY
171HMQC

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Sample preparation

Sample conditionspH: 5.2 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX/DMX / Manufacturer: Bruker / Model: AMX/DMX / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: AB INITIO SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: VIOLATIONS: NOE<0.5A, DIHE<5.0, BONDS<0.05A, ANGLES<5.0 IMPROPERS<5.0 / Conformers calculated total number: 500 / Conformers submitted total number: 20

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