SAXSdb — 1ddm

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

NUMB PROTEIN

Drosophila melanogaster

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 67–201	Fragment：PHOSPHOTYROSINE BINDING DOMAIN (PTB)	NUMB ASSOCIATE KINASE × 1	SOLUTION NMR NMR measurement conditions：pH 6；303 K；Ionic strength (raw mmCIF value) 50mM；Pressure 1 NMR sample composition：1MM PTB U-15N; 1MM NAK NA; 50MM PHOSPHATE BUFFER NA NMR sample composition：1MM PTB U-15N, 10% 13C; 1MM NAK NA; 50MM PHOSPHATE BUFFER NA NMR sample composition：1MM PTB U-15N, U-13C; 1MM NAK NA; 50MM PHOSPHATE BUFFER NA NMR sample composition：1MM PTB NA; 1MM NAK (G1 F2 F7 F10) 15N, 13C;; 50MM PHOSPHATE BUFFER NA	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 1DDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NMB DNUMB PTB DOMAIN COMPLEXED WITH A PHOSPHOTYROSINE PEPTIDE, NMR, ENSEMBLE OF STRUCTURES. Deposited 1998-10-29	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–205（154 aa） Fragment：PTB DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Pressure 1	Resolution not provided
5YI7 Crystal structure of drosophila Numb PTB domain and Pon peptide complex Deposited 2017-10-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 64–203（140 aa） Fragment：PTB domain	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.3；289 K；0,2M MgCl2.6H2O,25% PEG 3350,0.1M Bis-Tris	Resolution 1.70 Å R-free 0.218
5YI7 Crystal structure of drosophila Numb PTB domain and Pon peptide complex Deposited 2017-10-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 64–203（140 aa） Fragment：PTB domain	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.3；289 K；0,2M MgCl2.6H2O,25% PEG 3350,0.1M Bis-Tris	Resolution 1.70 Å R-free 0.218
5YI8 Crystal structure of drosophila Numb PTB domain and Pon peptide complex Deposited 2017-10-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 64–203（140 aa） Fragment：PTB domain	Not recorded	FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；289 K；0.1M sodium formate, 12% PEG 3350	Resolution 2.00 Å R-free 0.227

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

View Construct and Data Evidence

UniProt name	NUMB_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 67–201

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	1ddm
Deposition date deposition_date	1999-11-11
Structure title title	SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE
Keywords keywords	COMPLEX, SIGNAL TRANSDUCTION, PHOSPHOTYROSINE BINDING DOMAIN (PTB), ASYMMETRIC CELL DIVISION, SIGNALING PROTEIN-TRANSFERASE COMPLEX; SIGNALING PROTEIN/TRANSFERASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.33 Å
Radius of gyration Rg (electron density) rg_electron	14.86 Å
Forward intensity I(0) i0	1728050000.00
Molecular weight molecular_weight	330240.0 kDa
Excluded volume excluded_volume	403920 Å³
Envelope volume envelope_volume	38045 Å³
Hydration-shell volume shell_volume	18266 Å³
Envelope diameter envelope_diameter	57.8 Å
Shell Rg shell_rg	23.65 Å
Envelope Rg envelope_rg	17.50 Å
Shape Rg shape_rg	14.87 Å
Total Rg total_rg	14.97 Å
Total atoms total_atoms	45360
Residues n_residues	2920
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	50.9 Å
Rg (real space) rg_real	15.22 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.7280e+09
I(0) uncertainty (real space) i0_real_error	2.1130e+07
Rg (reciprocal space) rg_reciprocal	15.23 Å
I(0) (reciprocal space) i0_reciprocal	1728000000.0000
Solution quality estimate total_estimate	0.8717
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.144
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	967000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	NUMB PROTEIN
Molecular weight formula_weight	15277.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	45360

HQWQADEEAVRSATCSFSVKYLGCVEVFESRGMQVCEEALKVLRQSRRRPVRGLLHVSGDGLRVVDDETKGLIVDQTIEKVSFCAPDRNHERGFSYICRDGTTRRWMCHGFLACKDSGERLSHAVGCAFAVCLER

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NUMB ASSOCIATE KINASE
Molecular weight formula_weight	1277.4 kDa
EC 编号 ec_number	2.7.1.37
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GFSNMSFEDFP

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ddma_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.2 — Phosphotyrosine-binding domain (PTB)

CATH v4.4 (1 domains)

Domain ID domain_id	1ddmA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

fit	/app/data/saxs_computation/dd/1ddm/1ddm.fit
pddf	/app/data/pr_computation/dd/1ddm/1ddm.pr.out
profile	/app/data/saxs_computation/dd/1ddm/1ddm.dat

SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE

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

NUMB PROTEIN

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)