2r9k

Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide

Method: X-RAY DIFFRACTION Dmax: 83.9 Å Quality: GOOD

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

Beta-galactoside-specific lectin 1 chain B

Viscum album

UniProt P81446

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 302–564 Fragment:Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564 Beta-galactoside-specific lectin 1 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 4 GOL GLYCEROL × 4 CL CHLORIDE ION × 1 SGI 3-(4-hydroxyphenyl)propanamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 2.5;293 K;pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.70 Å R-free 0.267
2 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 302–564 Fragment:Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564 Beta-galactoside-specific lectin 1 × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 SO4 SULFATE ION × 8 GOL GLYCEROL × 8 CL CHLORIDE ION × 2 SGI 3-(4-hydroxyphenyl)propanamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 2.5;293 K;pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.70 Å R-free 0.267
3 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 302–564 Fragment:Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564 Beta-galactoside-specific lectin 1 × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 SO4 SULFATE ION × 8 GOL GLYCEROL × 8 CL CHLORIDE ION × 2 SGI 3-(4-hydroxyphenyl)propanamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 2.5;293 K;pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.70 Å R-free 0.267

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.

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ML1_VISAL
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–263; UniProt 302–564

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 2r9k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2r9k
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2r9k
Deposition date deposition_date2007-09-13
Structure title titleCrystal Structure of Misteltoe Lectin I in Complex with Phloretamide
Keywords keywordsML-I, phloretamide, Viscum album, Glycoprotein, Hydrolase, Lectin, Plant defense, Protein synthesis inhibitor, Toxin; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.04
Radius of gyration Rg (electron density) rg_electron25.06
Forward intensity I(0) i058196300.00
Molecular weight molecular_weight57745.0 kDa
Excluded volume excluded_volume71555 ų
Envelope volume envelope_volume84215 ų
Hydration-shell volume shell_volume28443 ų
Envelope diameter envelope_diameter87.0
Shell Rg shell_rg31.94
Envelope Rg envelope_rg25.16
Shape Rg shape_rg25.07
Total Rg total_rg25.76
Total atoms total_atoms4052
Residues n_residues510
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax83.9
Rg (real space) rg_real26.06
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real5.8200e+07
I(0) uncertainty (real space) i0_real_error8.8890e+05
Rg (reciprocal space) rg_reciprocal26.06
I(0) (reciprocal space) i0_reciprocal58200000.0000
Solution quality estimate total_estimate0.8948
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.400
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9695000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.949

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2r9ka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins
Domain ID domain_idd2r9kb1
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.2 — Ricin B-like lectins
Family Family familyb.42.2.1 — Ricin B-like
Domain ID domain_idd2r9kb2
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.2 — Ricin B-like lectins
Family Family familyb.42.2.1 — Ricin B-like

CATH v4.4 (4 domains)

Domain ID domain_id2r9kA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id2r9kA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
Domain ID domain_id2r9kB01
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id2r9kB02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50

8. Citations (1)

9. Files and Curves (10)