SAXSdb — 3pg7

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

Neurofibromin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PHOSPHATIDYLETHANOLAMINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PHOSPHATIDYLETHANOLAMINE × 1 PYROPHOSPHATE 2- × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–256； UniProt 1581–1837 Author chain B； PDBConstruct 1–256； UniProt 1581–1837

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	3pg7
Deposition date deposition_date	2010-10-31
Structure title title	Crystal structure of the H. sapiens NF1 SEC-PH domain (del1750 mutant)
Keywords keywords	SEC lipid binding domain, PH domain, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3pg7__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3pg7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pg7__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.39 Å
Rg (electron density)	19.25 Å
Total Rg	20.16 Å
Atom count	2048
Residues	256
Excluded volume	36731 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pg7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pg7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neurofibromin
Molecular weight formula_weight	29330.6 kDa
Mutation mutation	K1771 deletion mutant
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4362

KEEFKALKTLSIFYQAGTSKAGNPIFYYVARRFKTGQINGDLLIYHVLLTLKPYYAKPYEIVVDLTHTGPSNRFKTDFLSKWFVVFPGFAYDNVSAVYIYNCNSWVREYTKYHERLLTGLKGSKRLVFIDCPGKLAEHIEHEQQKLPAATLALEEDLKVFHNALKLAHKDTKVSIKVGSTAVQVTSAERTVLGQSVFLNDIYYASEIEEICLVDENQFTLTIANQGTPLTFMHQECEAIVQSIIHIRTRWELSQPD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	241

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3pg7A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
Homologous superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

Domain ID domain_id	3pg7A02
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)

Domain ID domain_id	3pg7B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
Homologous superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

Domain ID domain_id	3pg7B02
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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Unit-cell length a length_a	113.440 Å
Unit-cell length b length_b	113.440 Å
Unit-cell length c length_c	124.490 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.189 Å
Low-resolution limit resolution_low	36.000 Å
R factor r_factor	0.2104
R_work r_work	0.2083
R_free r_free	0.2488

Crystal structure of the H. sapiens NF1 SEC-PH domain (del1750 mutant)

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

Neurofibromin

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3pg7__assembly_1__model_1

3pg7__assembly_1__model_1 | I(q)

3pg7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the H. sapiens NF1 SEC-PH domain (del1750 mutant)

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

Neurofibromin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3pg7__assembly_1__model_1

3pg7__assembly_1__model_1 | I(q)

3pg7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)