SAXSdb — 3c5c

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

RAS-like protein 12

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	MAGNESIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 UNKNOWN ATOM OR ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 UNKNOWN ATOM OR ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 UNKNOWN ATOM OR ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9NYN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–187； UniProt 18–186 Author chain B； PDBConstruct 19–187； UniProt 18–186 Author chain C； PDBConstruct 19–187； UniProt 18–186 Author chain D； PDBConstruct 19–187； UniProt 18–186

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	3c5c
Deposition date deposition_date	2008-01-31
Structure title title	Crystal structure of human Ras-like, family 12 protein in complex with GDP
Keywords keywords	;ras, rasl12, gdp, gtpase, Structural Genomics Consortium, SGC, limited proteolysis, GTP-binding, Nucleotide-binding, SIGNALING PROTEIN ;; SIGNALING 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.

3c5c__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3c5c__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c5c__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.24 Å
Rg (electron density)	14.93 Å
Total Rg	16.02 Å
Atom count	1333
Residues	167
Excluded volume	23424 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c5c__assembly_1__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`3c5c__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3c5c__assembly_3__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
4	1	`3c5c__assembly_4__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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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	RAS-like protein 12
Molecular weight formula_weight	21430.1 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	5532

MHHHHHHSSGRENLYFQGPLEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADLDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARRE

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3c5ca_
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.37.1.0 — automated matches

Domain ID domain_id	d3c5cb_
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.37.1.0 — automated matches

Domain ID domain_id	d3c5cc1
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.37.1.0 — automated matches

Domain ID domain_id	d3c5cc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3c5cd_
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.37.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3c5cA00
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	3c5cB00
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	3c5cC00
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	3c5cD00
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

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Unit-cell length a length_a	34.040 Å
Unit-cell length b length_b	66.436 Å
Unit-cell length c length_c	71.943 Å
Unit-cell angle α angle_alpha	101.46 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	89.89 °
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	1.850 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2030
R_work r_work	0.2020
R_free r_free	0.2380

Crystal structure of human Ras-like, family 12 protein in complex with GDP

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

RAS-like protein 12

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

3c5c__assembly_2__model_1

3c5c__assembly_2__model_1 | I(q)

3c5c__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human Ras-like, family 12 protein in complex with GDP

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

RAS-like protein 12

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

3c5c__assembly_2__model_1

3c5c__assembly_2__model_1 | I(q)

3c5c__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)