SAXSdb — 2fj2

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 24–94 Chain B； UniProt 24–94	Not recorded	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 24–94 Chain D； UniProt 24–94	Not recorded	No other associated polymer	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

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 2FJ2	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 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state 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） 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 mutation/modification Different oligomeric state 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） 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state 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	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 mutation/modification Different oligomeric state 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
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 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 8 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 Author chain B； PDBConstruct 1–71； UniProt 24–94 Author chain C； PDBConstruct 1–71； UniProt 24–94 Author chain D； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2fj2
Deposition date deposition_date	2005-12-30
Structure title title	Crystal Structure of Viral Macrophage Inflammatory Protein-II
Keywords keywords	chemokine, herpesvirus, anti-HIV; CHEMOKINE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.85 Å
Radius of gyration Rg (electron density) rg_electron	30.80 Å
Forward intensity I(0) i0	13709300.00
Molecular weight molecular_weight	29772.0 kDa
Excluded volume excluded_volume	37765 Å³
Envelope volume envelope_volume	54681 Å³
Hydration-shell volume shell_volume	15618 Å³
Envelope diameter envelope_diameter	95.8 Å
Shell Rg shell_rg	36.04 Å
Envelope Rg envelope_rg	29.31 Å
Shape Rg shape_rg	30.81 Å
Total Rg total_rg	31.32 Å
Total atoms total_atoms	2084
Residues n_residues	270
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	98.0 Å
Rg (real space) rg_real	31.07 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	1.3710e+07
I(0) uncertainty (real space) i0_real_error	2.4270e+05
Rg (reciprocal space) rg_reciprocal	30.98 Å
I(0) (reciprocal space) i0_reciprocal	13710000.0000
Solution quality estimate total_estimate	0.6684
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.192
Kurtosis Kurtosis kurtosis	-1.028
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	595600.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.460; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.308; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2fj2a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d2fj2b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d2fj2c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d2fj2d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (4 domains)

Domain ID domain_id	2fj2A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2fj2B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2fj2C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2fj2D00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	45.650 Å
Unit-cell length b length_b	65.770 Å
Unit-cell length c length_c	45.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2480
R_work r_work	—
R_free r_free	0.3010

Description description	Viral macrophage inflammatory protein-II
Molecular weight formula_weight	8142.7 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2183

Crystal Structure of Viral Macrophage Inflammatory Protein-II

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

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

fit	/app/data/saxs_computation/fj/2fj2/2fj2.fit
pddf	/app/data/pr_computation/fj/2fj2/2fj2.pr.out
profile	/app/data/saxs_computation/fj/2fj2/2fj2.dat