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1mkf

VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68

Method: X-RAY DIFFRACTION Dmax: 101.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

M3

Murid herpesvirus 4

UniProt O41925

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 25–406 Chain B； UniProt 25–406 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；18% PEG4000, 100MM CACL2, 100MM IMIDAZOLE/MALIC ACID PH 5.1, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.273
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 25–406 Chain B； UniProt 25–406 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；18% PEG4000, 100MM CACL2, 100MM IMIDAZOLE/MALIC ACID PH 5.1, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.273

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 1MKF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ML0 VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1 Deposited 2002-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.282
1ML0 VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1 Deposited 2002-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.282
2NYZ Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1 Deposited 2006-11-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–406（382 aa）
Chain B 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；10% PEG 8000, 100 mM TRIS, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.272
2NZ1 Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1 Deposited 2006-11-22 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–406（382 aa）
Chain B 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；12% PEG 4000, 100 mM sodium acetate, 200 mM magnesium chloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.300
2NZ1 Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1 Deposited 2006-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain X 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；12% PEG 4000, 100 mM sodium acetate, 200 mM magnesium chloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.300

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O41925_MHV68
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–382； UniProt 25–406 Author chain B； PDBConstruct 1–382； UniProt 25–406

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 1mkf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1mkf
Deposition date deposition_date2002-08-29
Structure title titleVIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68
Keywords keywords;HERPESVIRUS, VIRAL IMMUNE EVASION, CHEMOKINE BINDING PROTEIN, DECOY RECEPTOR, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.63 Å
Radius of gyration Rg (electron density) rg_electron28.42 Å
Forward intensity I(0) i0109516000.00
Molecular weight molecular_weight81472.0 kDa
Excluded volume excluded_volume101420 ų
Envelope volume envelope_volume126720 ų
Hydration-shell volume shell_volume36273 ų
Envelope diameter envelope_diameter101.9 Å
Shell Rg shell_rg36.52 Å
Envelope Rg envelope_rg28.48 Å
Shape Rg shape_rg28.43 Å
Total Rg total_rg29.14 Å
Total atoms total_atoms5706
Residues n_residues742
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 dmax101.1 Å
Rg (real space) rg_real29.51 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real1.0950e+08
I(0) uncertainty (real space) i0_real_error1.7160e+06
Rg (reciprocal space) rg_reciprocal29.56 Å
I(0) (reciprocal space) i0_reciprocal109500000.0000
Solution quality estimate total_estimate0.8860
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.2 Å
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.555
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22920000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999
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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) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1mkfa_
Class classb — All beta proteins
Fold Fold foldb.116 — Viral chemokine binding protein m3
Superfamily Superfamily superfamilyb.116.1 — Viral chemokine binding protein m3
Family Family familyb.116.1.1 — Viral chemokine binding protein m3
Domain ID domain_idd1mkfb_
Class classb — All beta proteins
Fold Fold foldb.116 — Viral chemokine binding protein m3
Superfamily Superfamily superfamilyb.116.1 — Viral chemokine binding protein m3
Family Family familyb.116.1.1 — Viral chemokine binding protein m3

CATH v4.4 (4 domains)

Domain ID domain_id1mkfA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1330 —
Domain ID domain_id1mkfA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1340 — Chemokine-binding protein M3-like
Domain ID domain_id1mkfB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1330 —
Domain ID domain_id1mkfB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1340 — Chemokine-binding protein M3-like
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8. Citations (1)

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9. Files and Curves (10)