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1vmp

STRUCTURE OF THE ANTI-HIV CHEMOKINE VMIP-II

Method: SOLUTION NMR Dmax: 51.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ANTI-HIV CHEMOKINE MIP VII)

Human herpesvirus 8

UniProt Q98157

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 24–94 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.4；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure 1 Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1VMP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CM9 CRYSTAL STRUCTURE OF VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II Deposited 1999-05-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–94（74 aa）
Chain B 21–94（74 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.10 Å R-free 0.275
1HFF NMR solution structures of the vMIP-II 1-10 peptide from Kaposi's sarcoma-associated herpesvirus. Deposited 2000-12-01 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–33（10 aa） Fragment：RESIDUES 1-10
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；281 K；Ionic strength (raw mmCIF value) 20MM SODIUM ACETATE；Pressure 1
NMR sample composition 20MM SODIUM ACETATE, 1-2MM PEPTIDE, 1MM SODIUM AZIDE, 1MM DSS
Resolution not provided
1HFG NMR solution structure of vMIP-II 1-71 from Kaposi's sarcoma-associated herpesvirus (minimized average structure). Deposited 2000-12-01 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–94（71 aa） Fragment：RESIDUES 1-71
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；303 K；Pressure 1
Resolution not provided
1HFN NMR solution structures of vMIP-II 1-71 from Kaposi's sarcoma-associated herpesvirus. Deposited 2000-12-07 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–94（71 aa） Fragment：RESIDUES 1-71
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；303 K；Pressure 1
NMR sample composition 1MM DSS, 1MM NAN3, 20MM SODIUM ACETATE
Resolution not provided
1HHV SOLUTION STRUCTURE OF VIRUS CHEMOKINE VMIP-II Deposited 1998-12-06 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–94（74 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.25；308 K；Ionic strength (raw mmCIF value) 50 mM
NMR sample composition 90% H2O/10% D2O
Resolution not provided
2FHT Crystal Structure of Viral Macrophage Inflammatory Protein-II Deposited 2005-12-27 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–94（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1 M sodium citrate, 11% (w/v) PEG 4000, 11%(w/v) 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.331
2FJ2 Crystal Structure of Viral Macrophage Inflammatory Protein-II Deposited 2005-12-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–94（71 aa）
Chain B 24–94（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；100mM Sodium Citrate, 11% PEG 4000, 11% 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60
Resolution 2.30 Å R-free 0.301
2FJ2 Crystal Structure of Viral Macrophage Inflammatory Protein-II Deposited 2005-12-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 24–94（71 aa）
Chain D 24–94（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；100mM Sodium Citrate, 11% PEG 4000, 11% 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60
Resolution 2.30 Å R-free 0.301
4RWS Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community Target) Deposited 2014-12-05 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–94（71 aa）
Mutation：W5C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；100 mM sodium citrate pH 5.5, 28% PEG 400, 120 mM ammonium phosphate dibasic, 2-6% polypropylene P400, Lipidic cubic phase, temperature 293K
Resolution 3.10 Å R-free 0.274

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VMI2_HHV8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–71； UniProt 24–94

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1vmp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vmp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vmp
Deposition date deposition_date1999-03-25
Structure title titleSTRUCTURE OF THE ANTI-HIV CHEMOKINE VMIP-II
Keywords keywords;VMIP-II, CHEMOKINE, MONOMER, SARCOMA, HERPESVIRUS, HHV-8, KAPOSI'S, ANTIVIRAL PROTEIN ;; ANTIVIRAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.84 Å
Radius of gyration Rg (electron density) rg_electron12.90 Å
Forward intensity I(0) i01445210.00
Molecular weight molecular_weight8139.0 kDa
Excluded volume excluded_volume10313 ų
Envelope volume envelope_volume12028 ų
Hydration-shell volume shell_volume8532 ų
Envelope diameter envelope_diameter51.3 Å
Shell Rg shell_rg17.77 Å
Envelope Rg envelope_rg13.97 Å
Shape Rg shape_rg12.90 Å
Total Rg total_rg14.20 Å
Total atoms total_atoms1166
Residues n_residues71
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax51.3 Å
Rg (real space) rg_real13.88 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real1.4450e+06
I(0) uncertainty (real space) i0_real_error1.8120e+04
Rg (reciprocal space) rg_reciprocal13.88 Å
I(0) (reciprocal space) i0_reciprocal1445000.0000
Solution quality estimate total_estimate0.7399
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary15.6 Å
Skewness Skewness skewness0.491
Kurtosis Kurtosis kurtosis0.138
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha263200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.603; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.814; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1vmpa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.9 — IL8-like
Superfamily Superfamily superfamilyd.9.1 — Interleukin 8-like chemokines
Family Family familyd.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (1 domains)

Domain ID domain_id1vmpA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)