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- PDB-1hhv: SOLUTION STRUCTURE OF VIRUS CHEMOKINE VMIP-II -

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Basic information

Entry
Database: PDB / ID: 1hhv
TitleSOLUTION STRUCTURE OF VIRUS CHEMOKINE VMIP-II
ComponentsVIRUS CHEMOKINE VMIP-II
KeywordsVIRAL PROTEIN / VMIP-II / VIRUS CHEMOKINE / KSHV(HUMAN HERPESVIRUS 8) / RECEPTOR BINDING
Function / homology
Function and homology information


CXCR chemokine receptor binding / chemokine activity / immune response / protein-containing complex / extracellular space
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Viral macrophage inflammatory protein 2
Similarity search - Component
MethodSOLUTION NMR / TORSIONAL ANGLE MOLECULAR DYNAMICS
AuthorsShao, W. / Fernandez, E. / Navenot, J.M. / Wilken, J. / Thompson, D.A. / Pepiper, S. / Schweitzer, B.I. / Lolis, E.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: CCR2 and CCR5 receptor-binding properties of herpesvirus-8 vMIP-II based on sequence analysis and its solution structure
Authors: Shao, W. / Fernandez, E. / Sachpatzidis, A. / Wilken, J. / Thompson, D.A. / Schweitzer, B.I. / Lolis, E.
#1: Journal: FEBS Lett. / Year: 1998
Title: Accessibility of selenomethionine proteins by total chemical synthesis: Structural studies of human herpesvirus-8 MIP-II
Authors: Shao, W. / Fernandez, E. / Wilken, J. / Thompson, D.A. / Siani, M.A. / West, J. / Lolis, E. / Schweitzer, B.I.
History
DepositionDec 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VIRUS CHEMOKINE VMIP-II


Theoretical massNumber of molelcules
Total (without water)8,4631
Polymers8,4631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 80LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
Representative

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Components

#1: Protein VIRUS CHEMOKINE VMIP-II / ORF K4 / vMIP-II / macrophage inflammatory protein 1-alpha homolog


Mass: 8462.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE from Human herpesvirus 8 / References: UniProt: Q98157

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131HSQC
141DQF-COSY
NMR detailsText: THE STRUCTURES WERE DETERMINED USING TWO- DIMENSIONAL HOMO- AND HETERO-NUCLEAR NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 3.25 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851BRUNGERstructure calculation
RefinementMethod: TORSIONAL ANGLE MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
Conformers calculated total number: 80 / Conformers submitted total number: 25

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