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- PDB-1hff: NMR solution structures of the vMIP-II 1-10 peptide from Kaposi's... -

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Basic information

Entry
Database: PDB / ID: 1hff
TitleNMR solution structures of the vMIP-II 1-10 peptide from Kaposi's sarcoma-associated herpesvirus.
ComponentsVIRAL MACROPHAGE INFLAMMATORY PROTEIN-II
KeywordsCHEMOKINE / CXCR4 / ANATAGONIST / VMIP-II
Function / homology
Function and homology information


CXCR chemokine receptor binding / eosinophil chemotaxis / 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
Similarity search - Domain/homology
Viral macrophage inflammatory protein 2
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 8
MethodSOLUTION NMR / simulated annealing
AuthorsCrump, M.P. / Elisseeva, E. / Gong, J.H. / Clark-Lewis, I. / Sykes, B.D.
CitationJournal: FEBS Lett. / Year: 2001
Title: Structure/Function of Human Herpesvirus-8 Mip-II (1-71) and the Antagonist N-Terminal Segment (1-10)
Authors: Crump, M.P. / Elisseeva, E. / Gong, J.H. / Clark-Lewis, I. / Sykes, B.D.
History
DepositionDec 1, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II


Theoretical massNumber of molelcules
Total (without water)1,1691
Polymers1,1691
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)55 / 55LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein/peptide VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II / VMIP-II / VMIP-1B


Mass: 1169.313 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-10 / Source method: obtained synthetically / Source: (synth.) 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
111DQF-COSY
121TOCSY
131NOESY
NMR detailsText: SEE PAPER FOR FURTHER EXPERIMENTAL DETAILS.

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Sample preparation

DetailsContents: 20MM SODIUM ACETATE, 1-2MM PEPTIDE, 1MM SODIUM AZIDE, 1MM DSS
Sample conditionsIonic strength: 20MM SODIUM ACETATE / pH: 5 / Pressure: 1 atm / Temperature: 281 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 55 / Conformers submitted total number: 55

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