SAXSdb — 1d1z

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

SAP SH2 DOMAIN

Homo sapiens

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–104 Chain B； UniProt 1–104 Chain C； UniProt 1–104 Chain D； UniProt 1–104	Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–104 Chain B； UniProt 1–104 Chain C； UniProt 1–104 Chain D； UniProt 1–104	Fragment：SAP SH2 DOMAIN (RESIDUES 1-104)	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

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 1D1Z	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 oligomeric state Different ligand/ion 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
1D4W CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHOSPHOPEPTIDE Deposited 1999-10-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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	Mutation：RESIDUES 1-104	No recorded non-water small molecule	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
1D4W CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHOSPHOPEPTIDE Deposited 1999-10-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–104（104 aa） Fragment：SH2 DOMAIN	Mutation：RESIDUES 1-104	No recorded non-water small molecule	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
1KA6 SAP/SH2D1A bound to peptide n-pY Deposited 2001-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 Author chain C； PDBConstruct 1–104； UniProt 1–104 Author chain D； PDBConstruct 1–104； UniProt 1–104

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d1z
Deposition date deposition_date	1999-09-22
Structure title title	CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP
Keywords keywords	SH2 DOMAINS, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	26.70 Å
Radius of gyration Rg (electron density) rg_electron	25.69 Å
Forward intensity I(0) i0	33204900.00
Molecular weight molecular_weight	45376.0 kDa
Excluded volume excluded_volume	57221 Å³
Envelope volume envelope_volume	73679 Å³
Hydration-shell volume shell_volume	24305 Å³
Envelope diameter envelope_diameter	84.0 Å
Shell Rg shell_rg	32.45 Å
Envelope Rg envelope_rg	25.43 Å
Shape Rg shape_rg	25.71 Å
Total Rg total_rg	26.45 Å
Total atoms total_atoms	3195
Residues n_residues	397
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	82.0 Å
Rg (real space) rg_real	26.63 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.3200e+07
I(0) uncertainty (real space) i0_real_error	4.8580e+05
Rg (reciprocal space) rg_reciprocal	26.66 Å
I(0) (reciprocal space) i0_reciprocal	33210000.0000
Solution quality estimate total_estimate	0.9058
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.119
Kurtosis Kurtosis kurtosis	-0.759
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9211000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SAP SH2 DOMAIN
Molecular weight formula_weight	11702.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3823

MDAVAVYHGKISRETGEKLLLATGLDGSYLLRDSESVPGVYCLCVLYHGYIYTYRVSQTETGSWSAETAPGVHKRYFRKIKNLISAFQKPDQGIVIPLQYPVEK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	628

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d1za_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1d1zb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1d1zc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1d1zd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

CATH v4.4 (4 domains)

Domain ID domain_id	1d1zA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1d1zB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1d1zC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1d1zD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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8. Citations (2)

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Unit-cell length a length_a	32.480 Å
Unit-cell length b length_b	62.270 Å
Unit-cell length c length_c	65.090 Å
Unit-cell angle α angle_alpha	65.71 °
Unit-cell angle β angle_beta	78.67 °
Unit-cell angle γ angle_gamma	89.66 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1390
R_work r_work	0.1390
R_free r_free	0.1870

fit	/app/data/saxs_computation/d1/1d1z/1d1z.fit
pddf	/app/data/pr_computation/d1/1d1z/1d1z.pr.out
profile	/app/data/saxs_computation/d1/1d1z/1d1z.dat

CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP

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

SAP SH2 DOMAIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction