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2n6f

Structure of Pleiotrophin

Method: SOLUTION NMR Dmax: 101.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pleiotrophin

Homo sapiens

UniProt P21246

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 33–168 Fragment：UNP residues 33-168 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition：0.6 mM [U-100% 13C; U-100% 15N] PTN, 10 % v/v D2O, 10 mM MES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O 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 2N6F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8VOH HADDOCK models of human alphaM I-domain bound to the the N-terminal domain of the cytokine pleiotrophin Deposited 2024-01-15 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 33–90（58 aa） Fragment：N-terminal domain, residues 33-90
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1
NMR sample composition 0.2 mM [U-13C; U-15N] human alphaM I-domain, 1 mM The N-terminal domain of pleiotrophin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] human alphaM I-domain, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] The N-terminal domain of pleiotrophin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8VOI HADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin Deposited 2024-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 90–146（57 aa） Fragment：C-terminal domain, residues 90-146
Not recorded MG MAGNESIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1
NMR sample composition 0.3 mM [U-100% 13C; U-100% 15N] active human alphaM I-domain, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] The C-terminal Domain of Pleiotrophin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM The C-terminal Domain of Pleiotrophin, 0.2 mM [U-100% 13C; U-100% 15N; U-80% 2H] active human alphaM I-domain, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTN_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–136； UniProt 33–168

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 2n6f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2n6f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2n6f
Deposition date deposition_date2015-08-20
Structure title titleStructure of Pleiotrophin
Keywords keywordscytokine, glycosaminoglycan-binding protein, mitogen, angiogenesis, Heparin-binding Protein; Heparin-binding 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_guinier27.04 Å
Radius of gyration Rg (electron density) rg_electron26.79 Å
Forward intensity I(0) i0378670000.00
Molecular weight molecular_weight153310.0 kDa
Excluded volume excluded_volume190420 ų
Envelope volume envelope_volume163010 ų
Hydration-shell volume shell_volume43341 ų
Envelope diameter envelope_diameter111.8 Å
Shell Rg shell_rg38.49 Å
Envelope Rg envelope_rg31.17 Å
Shape Rg shape_rg26.76 Å
Total Rg total_rg27.59 Å
Total atoms total_atoms21630
Residues n_residues1360
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 dmax101.8 Å
Rg (real space) rg_real27.17 Å
Rg uncertainty (real space) rg_real_error1.10 Å
I(0) (real space) i0_real3.7870e+08
I(0) uncertainty (real space) i0_real_error5.6930e+06
Rg (reciprocal space) rg_reciprocal27.13 Å
I(0) (reciprocal space) i0_reciprocal378700000.0000
Solution quality estimate total_estimate0.8316
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.3 Å
Skewness Skewness skewness0.410
Kurtosis Kurtosis kurtosis-0.209
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha973400.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.713; Smooth: 0.999
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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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8. Citations (1)

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9. Files and Curves (10)