SAXSdb — 1tu4

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

Ras-related protein Rab-5A

Homo sapiens

UniProt P20339

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	COBALT (II) ION × 3 GUANOSINE-5'-DIPHOSPHATE × 2 SULFATE ION × 2 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 SULFATE ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 SULFATE ION × 4 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 8	COBALT (II) ION × 12 GUANOSINE-5'-DIPHOSPHATE × 8 SULFATE ION × 12 water × 8	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 6 GUANOSINE-5'-DIPHOSPHATE × 4 SULFATE ION × 6 water × 4	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 6 GUANOSINE-5'-DIPHOSPHATE × 4 SULFATE ION × 4 water × 4	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 6 GUANOSINE-5'-DIPHOSPHATE × 4 SULFATE ION × 8 water × 4	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	COBALT (II) ION × 3 GUANOSINE-5'-DIPHOSPHATE × 2 SULFATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB5A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–171； UniProt 15–184 Author chain B； PDBConstruct 2–171； UniProt 15–184 Author chain C； PDBConstruct 2–171； UniProt 15–184 Author chain D； PDBConstruct 2–171； UniProt 15–184

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	1tu4
Deposition date deposition_date	2004-06-24
Structure title title	Crystal Structure of Rab5-GDP Complex
Keywords keywords	RAB5, GTPASE, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

1tu4__assembly_1__model_1

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

Download this curve (.dat)

1tu4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tu4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.49 Å
Rg (electron density)	15.20 Å
Total Rg	16.32 Å
Atom count	1355
Residues	165
Excluded volume	24134 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tu4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tu4__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1tu4__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1tu4__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1tu4__assembly_5__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1tu4__assembly_6__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1tu4__assembly_7__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1tu4__assembly_8__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`1tu4__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`1tu4__assembly_10__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	Ras-related protein Rab-5A
Molecular weight formula_weight	19306.3 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	5659

MGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN

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	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	6

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	309

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1tu4a_
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

Domain ID domain_id	d1tu4b_
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

Domain ID domain_id	d1tu4c_
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

Domain ID domain_id	d1tu4d_
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 (4 domains)

Domain ID domain_id	1tu4A00
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	1tu4B00
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	1tu4C00
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	1tu4D00
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	84.900 Å
Unit-cell length b length_b	84.900 Å
Unit-cell length c length_c	199.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	29.610 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2740

Crystal Structure of Rab5-GDP Complex

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

Ras-related protein Rab-5A

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

1tu4__assembly_1__model_1

1tu4__assembly_1__model_1 | I(q)

1tu4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Rab5-GDP Complex

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

Ras-related protein Rab-5A

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

1tu4__assembly_1__model_1

1tu4__assembly_1__model_1 | I(q)

1tu4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)