SAXSdb — 1hff

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1. Protein Identity and Related Structures Protein Identity & Related Structures

VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II

OrganismNot specified

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 24–33	Fragment：RESIDUES 1-10	No other associated polymer	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

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 1HFF	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
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
1VMP STRUCTURE OF THE ANTI-HIV CHEMOKINE VMIP-II Deposited 1999-03-25	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–94（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.4；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure 1	Resolution not provided
2FHT Crystal Structure of Viral Macrophage Inflammatory Protein-II Deposited 2005-12-27	Different construct 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 construct 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_KSHV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–10； UniProt 24–33

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hff
Deposition date deposition_date	2000-12-01
Structure title title	NMR solution structures of the vMIP-II 1-10 peptide from Kaposi's sarcoma-associated herpesvirus.
Keywords keywords	CHEMOKINE, CXCR4, ANATAGONIST, VMIP-II; CHEMOKINE
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	7.34 Å
Radius of gyration Rg (electron density) rg_electron	8.22 Å
Forward intensity I(0) i0	65369300.00
Molecular weight molecular_weight	64202.0 kDa
Excluded volume excluded_volume	79032 Å³
Envelope volume envelope_volume	9027 Å³
Hydration-shell volume shell_volume	7121 Å³
Envelope diameter envelope_diameter	36.6 Å
Shell Rg shell_rg	16.38 Å
Envelope Rg envelope_rg	12.05 Å
Shape Rg shape_rg	8.08 Å
Total Rg total_rg	8.99 Å
Total atoms total_atoms	8965
Residues n_residues	550
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	20.0 Å
Rg (real space) rg_real	7.03 Å
Rg uncertainty (real space) rg_real_error	0.03 Å
I(0) (real space) i0_real	6.2880e+07
I(0) uncertainty (real space) i0_real_error	3.4800e+05
Rg (reciprocal space) rg_reciprocal	7.46 Å
I(0) (reciprocal space) i0_reciprocal	65370000.0000
Solution quality estimate total_estimate	0.6604
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	6.8 Å
Skewness Skewness skewness	0.268
Kurtosis Kurtosis kurtosis	-0.783
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	7.9860
Highest regularization parameter α highest_alpha	755.6000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 1.000; Stabil: 0.969; Sysdev: 0.000; Positv: 1.000; Valcen: 0.679; 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) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1hffa_
Class class	j — Peptides
Fold Fold fold	j.73 — VMIP-II fragment
Superfamily Superfamily superfamily	j.73.1 — VMIP-II fragment
Family Family family	j.73.1.1 — VMIP-II fragment

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II
Molecular weight formula_weight	1169.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8965

fit	/app/data/saxs_computation/hf/1hff/1hff.fit
pddf	/app/data/pr_computation/hf/1hff/1hff.pr.out
profile	/app/data/saxs_computation/hf/1hff/1hff.dat

NMR solution structures of the vMIP-II 1-10 peptide from Kaposi's sarcoma-associated herpesvirus.

1. Protein Identity and Related Structures Protein Identity & Related Structures

VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)