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1d4w

CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHOSPHOPEPTIDE

Method: X-RAY DIFFRACTION Dmax: 99.4 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

T CELL SIGNAL TRANSDUCTION MOLECULE SAP

Homo sapiens

UniProt O60880

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–104 Fragment：SH2 DOMAIN Mutation：RESIDUES 1-104 SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE × 1 （Q13291） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；30% PEG 8000, 20% GLYCEROL, 100 MM SODIUM CITRATE, 10MM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 1.80 Å R-free 0.240
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–104 Fragment：SH2 DOMAIN Mutation：RESIDUES 1-104 SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE × 1 （Q13291） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；30% PEG 8000, 20% GLYCEROL, 100 MM SODIUM CITRATE, 10MM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 1.80 Å R-free 0.240

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 1D4W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D1Z CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP Deposited 1999-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Chain B 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Chain C 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Chain D 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；1.64 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE, PH 5.6, AND 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 1.40 Å R-free 0.187
1D1Z CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP Deposited 1999-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Chain B 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Chain C 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Chain D 1–104（104 aa） Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)
Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；1.64 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE, PH 5.6, AND 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 1.40 Å R-free 0.187
1D4T CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH A SLAM PEPTIDE Deposited 1999-10-06 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa） Fragment：SH2 DOMAIN (RESIDUES 1-104)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；30% PEG 8000, 20% GLYCEROL, 100 MM HEPES PH 8.0, AND 100 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 1.10 Å R-free 0.165
1KA6 SAP/SH2D1A bound to peptide n-pY Deposited 2001-10-31 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–128（128 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient
NMR sample composition 1 mM SAP U-15N, 13C; 1mM n-pY; 20 mM phosphate buffer, 100mM NaCl | 90% H2O/10% D2O
Resolution not provided
1KA7 SAP/SH2D1A bound to peptide n-Y-c Deposited 2001-10-31 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–128（128 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient
NMR sample composition 1 mM SAP U-15N, 13C; 1mM n-pY; 20 mM phosphate buffer, 100mM NaCl | 90% H2O/10% D2O
Resolution not provided
1M27 Crystal structure of SAP/FynSH3/SLAM ternary complex Deposited 2002-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–104（104 aa）
Not recorded FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；297 K；Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.50 Å R-free 0.266

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SH21A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain B； PDBConstruct 1–104； UniProt 1–104

SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE

OrganismNot specified

UniProt Q13291

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 276–286 Fragment：CYTOPLASMIC TAIL SYNTHETIC PHOSPOPEPTIDE Non-standard monomer：Yes (specific site not provided by mmCIF) T CELL SIGNAL TRANSDUCTION MOLECULE SAP × 1 （O60880） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；30% PEG 8000, 20% GLYCEROL, 100 MM SODIUM CITRATE, 10MM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 1.80 Å R-free 0.240
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 276–286 Fragment：CYTOPLASMIC TAIL SYNTHETIC PHOSPOPEPTIDE Non-standard monomer：Yes (specific site not provided by mmCIF) T CELL SIGNAL TRANSDUCTION MOLECULE SAP × 1 （O60880） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；30% PEG 8000, 20% GLYCEROL, 100 MM SODIUM CITRATE, 10MM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 1.80 Å R-free 0.240

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 1D4W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D4T CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH A SLAM PEPTIDE Deposited 1999-10-06 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 276–286（11 aa） Fragment：SLAM TAIL PEPTIDE (RESIDUES 276 TO 286)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；30% PEG 8000, 20% GLYCEROL, 100 MM HEPES PH 8.0, AND 100 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 1.10 Å R-free 0.165
1KA6 SAP/SH2D1A bound to peptide n-pY Deposited 2001-10-31 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 275–282（8 aa） Fragment：Cytoplasmic Region (residues 275-282)
Mutation：K275R Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient
NMR sample composition 1 mM SAP U-15N, 13C; 1mM n-pY; 20 mM phosphate buffer, 100mM NaCl | 90% H2O/10% D2O
Resolution not provided
1KA7 SAP/SH2D1A bound to peptide n-Y-c Deposited 2001-10-31 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 275–286（12 aa） Fragment：Cytoplasmic region (residues 275-286)
Mutation：K275R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient
NMR sample composition 1 mM SAP U-15N, 13C; 1mM n-pY; 20 mM phosphate buffer, 100mM NaCl | 90% H2O/10% D2O
Resolution not provided
1M27 Crystal structure of SAP/FynSH3/SLAM ternary complex Deposited 2002-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 276–286（11 aa） Fragment：SLAM peptide (residues 276-286)
Not recorded FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；297 K；Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.50 Å R-free 0.266

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SLAF1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–11； UniProt 276–286 Author chain D； PDBConstruct 1–11； UniProt 276–286

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 1d4w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d4w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d4w
Deposition date deposition_date1999-10-06
Structure title titleCRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHOSPHOPEPTIDE
Keywords keywordsSH2 DOMAIN, PHOSPHOTYROSINE RECOGNIITON, PEPTIDE RECOGNITION, SIGNAL TRANSDUCTION, LYMPHOPROLIFERATIVE DISEASE, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier32.56 Å
Radius of gyration Rg (electron density) rg_electron32.04 Å
Forward intensity I(0) i09789530.00
Molecular weight molecular_weight25393.0 kDa
Excluded volume excluded_volume32096 ų
Envelope volume envelope_volume45161 ų
Hydration-shell volume shell_volume11757 ų
Envelope diameter envelope_diameter101.9 Å
Shell Rg shell_rg39.37 Å
Envelope Rg envelope_rg30.45 Å
Shape Rg shape_rg32.03 Å
Total Rg total_rg32.79 Å
Total atoms total_atoms1790
Residues n_residues224
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 dmax99.4 Å
Rg (real space) rg_real33.04 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real9.7900e+06
I(0) uncertainty (real space) i0_real_error1.5340e+05
Rg (reciprocal space) rg_reciprocal32.85 Å
I(0) (reciprocal space) i0_reciprocal9788000.0000
Solution quality estimate total_estimate0.4314
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.3 Å
Skewness Skewness skewness0.178
Kurtosis Kurtosis kurtosis-1.455
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1409000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.002; Stabil: 0.998; Sysdev: 0.242; Positv: 1.000; Valcen: 0.020; Smooth: 0.858
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d4wa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain
Domain ID domain_idd1d4wb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain

CATH v4.4 (2 domains)

Domain ID domain_id1d4wA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id1d4wB00
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 (2)

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9. Files and Curves (10)