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2l6k

Solution Structure of a Nonphosphorylated Peptide Recognizing Domain

Method: SOLUTION NMR Dmax: 51.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tensin-like C1 domain-containing phosphatase

Homo sapiens

UniProt Q63HR2

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 1135–1248 Fragment：Nonphosphorylated Peptide Recognizing Domain, SH2 domain, UNP residues 2-115 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition：0.6mM [U-99% 13C; U-99% 15N] Protein Domain; 150mM sodium chloride; 20mM sodium phosphate; 2mM EDTA; 50mM Arginine; 50mM glutamine; 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 2L6K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KNO NMR Solution Structure of SH2 Domain of the Human Tensin Like C1 Domain Containing Phosphatase (TENC1) Deposited 2009-08-27 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1135–1249（115 aa） Fragment：Src Homolog 2 domain of TENC1, UNP residues 1135-1249
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient
NMR sample composition 1mM [U-100% 13C] SH2-1, 100mM sodium acetate-2, 100mM sodium chloride-3, 100% D2O | 100% D2O
NMR sample composition 1mM [U-100% 15N] SH2-4, 100mM sodium acetate-5, 100mM sodium chloride-6, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM [U-100% 13C; U-100% 15N] SH2-7, 100mM sodium acetate-8, 100mM sodium chloride-9, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM SH2-10, 100mM sodium acetate-11, 100mM sodium chloride-12, 100% D2O | 100% D2O
Resolution not provided
2LOZ The novel binding mode of DLC1 and Tensin2 PTB domain Deposited 2012-01-29 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1263–1409（147 aa） Fragment：PTB domain, UNP residues 1263-1409
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient
NMR sample composition 0.6-0.8 mM [U-100% 13C; U-100% 15N] Tensin2-1, 1.2-1.4 mM DLC1-2, 100 mM potassium phosphate-3, 100 mM potassium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.2-1.4 mM Tensin2-6, 0.6-0.8 mM [U-100% 13C; U-100% 15N] DLC1-7, 100 mM potassium phosphate-8, 100 mM potassium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6-0.8 mM [U-100% 13C] Tensin2-11, 1.2-1.4 mM DLC1-12, 100 mM potassium phosphate-13, 100 mM potassium chloride-14, 1 mM EDTA-15, 100% D2O | 100% D2O
NMR sample composition 1.2-1.4 mM Tensin2-16, 0.6-0.8 mM [U-100% 13C] DLC1-17, 100 mM potassium phosphate-18, 100 mM potassium chloride-19, 1 mM EDTA-20, 100% D2O | 100% D2O
Resolution not provided
3HQC Crystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1) Deposited 2009-06-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1264–1409（146 aa） Fragment：Phosphotyrosine Binding Domain, PTB, residues 1264-1409
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 ACT ACETATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；294 K；100mM Sodium Acetate pH 4 + 2% Glycerol + 2000mM Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.80 Å R-free 0.242

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

View Construct and Data Evidence
UniProt name TENC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–115； UniProt 1135–1248

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 2l6k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2l6k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2l6k
Deposition date deposition_date2010-11-22
Structure title titleSolution Structure of a Nonphosphorylated Peptide Recognizing Domain
Keywords keywordsANTITUMOR PROTEIN, CELL ADHESION, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.50 Å
Radius of gyration Rg (electron density) rg_electron14.35 Å
Forward intensity I(0) i0798851000.00
Molecular weight molecular_weight251730.0 kDa
Excluded volume excluded_volume320060 ų
Envelope volume envelope_volume33507 ų
Hydration-shell volume shell_volume16551 ų
Envelope diameter envelope_diameter57.4 Å
Shell Rg shell_rg23.19 Å
Envelope Rg envelope_rg17.70 Å
Shape Rg shape_rg14.33 Å
Total Rg total_rg14.60 Å
Total atoms total_atoms32540
Residues n_residues2300
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 dmax51.1 Å
Rg (real space) rg_real14.43 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real7.9890e+08
I(0) uncertainty (real space) i0_real_error9.1270e+06
Rg (reciprocal space) rg_reciprocal14.44 Å
I(0) (reciprocal space) i0_reciprocal798900000.0000
Solution quality estimate total_estimate0.8487
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.4 Å
Skewness Skewness skewness0.160
Kurtosis Kurtosis kurtosis-0.258
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha317800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.683; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.995
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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

CATH v4.4 (1 domains)

Domain ID domain_id2l6kA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
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8. Citations (1)

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9. Files and Curves (10)