SAXSdb — 3ddc

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

GTPase HRas

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ras association domain-containing family protein 5 × 2 （Q5EBH1） MAGNESIUM ION × 2 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ras association domain-containing family protein 5 × 1 （Q5EBH1） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RASH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 1–166

Ras association domain-containing family protein 5

Mus musculus

UniProt Q5EBH1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	GTPase HRas × 2 （P01112） MAGNESIUM ION × 2 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	GTPase HRas × 1 （P01112） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RASF5_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–163； UniProt 200–357

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	3ddc
Deposition date deposition_date	2008-06-05
Structure title title	Crystal Structure of NORE1A in Complex with RAS
Keywords keywords	;Oncogene, Tumorsuppressor, Ubiquitin Fold, RAS effector, RAP1, H-RAS, RASSF1, RASSF5, RAPL, NORE1, GMPPNP, Adaptor, Apoptosis, Microtubules, HYDROLASE-APOPTOSIS COMPLEX, Disease mutation, Golgi apparatus, GTP-binding, Lipoprotein, Membrane, Methylation, Nucleotide-binding, Palmitate, Prenylation, Proto-oncogene, Anti-oncogene, Cell cycle, Metal-binding, Microtubule, Phorbol-ester binding, Zinc-finger ;; HYDROLASE/APOPTOSIS
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.

3ddc__assembly_1__model_1

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

Download this curve (.dat)

3ddc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ddc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.26 Å
Rg (electron density)	27.02 Å
Total Rg	27.76 Å
Atom count	4854
Residues	598
Excluded volume	86581 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ddc__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ddc__assembly_2__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	GTPase HRas
Molecular weight formula_weight	18889.3 kDa
EC 编号 ec_number	3.6.5.2
Mutation mutation	D30E, E31K
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	2542

MTEYKLVVVGAGGVGKSALTIQLIQNHFVEKYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

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 polymer

Description description	Ras association domain-containing family protein 5
Molecular weight formula_weight	18448.4 kDa
Mutation mutation	L285M, K302D
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSPEFPPTIQEIKQKIDSYNSREKHCLGMKLSEDGTYTGFIKVHLKLRRPVTVPAGIRPQSIYDAIKEVNPAATTDKRTSFYLPLDAIKQMHISSTTTVSEVIQGLLDKFMVVDNPQKFALFKRIHKDGQVLFQKLSIADYPLYLRLLAGPDTDVLSFVLKEN

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ddca_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (2 domains)

Domain ID domain_id	3ddcA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3ddcB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	79.600 Å
Unit-cell length b length_b	88.000 Å
Unit-cell length c length_c	56.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.590 Å
R factor r_factor	0.1950
R_work r_work	0.1930
R_free r_free	0.2300

Crystal Structure of NORE1A in Complex with RAS

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

GTPase HRas

State in the Current Structure

Other States of the Same Protein in the Database

Ras association domain-containing family protein 5

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

3ddc__assembly_1__model_1

3ddc__assembly_1__model_1 | I(q)

3ddc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of NORE1A in Complex with RAS

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

GTPase HRas

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras association domain-containing family protein 5

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

3ddc__assembly_1__model_1

3ddc__assembly_1__model_1 | I(q)

3ddc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)