SAXSdb — 1z0k

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

GTP-binding protein

Homo sapiens

UniProt P20338

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	FYVE-finger-containing Rab5 effector protein rabenosyn-5 × 1 （Q59EY8） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	FYVE-finger-containing Rab5 effector protein rabenosyn-5 × 1 （Q59EY8） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB4A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–172； UniProt 2–172 Author chain C； PDBConstruct 2–172； UniProt 2–172

FYVE-finger-containing Rab5 effector protein rabenosyn-5

Homo sapiens

UniProt Q59EY8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GTP-binding protein × 1 （P20338） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	GTP-binding protein × 1 （P20338） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q59EY8_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–69； UniProt 440–503 Author chain D； PDBConstruct 6–69； UniProt 440–503

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	1z0k
Deposition date deposition_date	2005-03-01
Structure title title	Structure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of Rabenosyn-5
Keywords keywords	Rab GTPases, Rab4, Rabenosyn, effector complex, vesicular trafficking, 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.

1z0k__assembly_2__model_1

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

Download this curve (.dat)

1z0k__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z0k__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.20 Å
Rg (electron density)	17.02 Å
Total Rg	17.99 Å
Atom count	1828
Residues	229
Excluded volume	32231 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z0k__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1z0k__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 (6)

Entity 1 Entity 1 polymer

Description description	GTP-binding protein
Molecular weight formula_weight	19392.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4108

GSETYDFLFKFLVIGNAGTGKSCLLHQFIEKKFKDDSNHTIGVEFGSKIINVGGKYVKLQIWDTAGLERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQENELMFLETSALTGEDVEEAFVQCARKILNK

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	FYVE-finger-containing Rab5 effector protein rabenosyn-5
Molecular weight formula_weight	7716.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPLGSAEGWLPLSGGQGQSEDSDPLLQQIHNITSFIRQAKAAGRMDEVRTLQENLRQLQDEYDQQQTEK

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 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	2

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	457

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1z0ka1
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	d1z0kb1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.19 — Rabenosyn-5 Rab-binding domain-like
Family Family family	a.2.19.1 — Rabenosyn-5 Rab-binding domain-like

Domain ID domain_id	d1z0kc_
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	d1z0kd_
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.19 — Rabenosyn-5 Rab-binding domain-like
Family Family family	a.2.19.1 — Rabenosyn-5 Rab-binding domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	1z0kA01
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	1z0kB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	860 — DNA Excision Repair, Uvrb; Chain A
Homologous superfamily homologous superfamily	20 — Rabenosyn, Rab binding domain

Domain ID domain_id	1z0kC01
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	1z0kD00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	860 — DNA Excision Repair, Uvrb; Chain A
Homologous superfamily homologous superfamily	20 — Rabenosyn, Rab binding domain

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Unit-cell length a length_a	81.440 Å
Unit-cell length b length_b	81.440 Å
Unit-cell length c length_c	137.639 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	12

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

Resolution resolution	1.920 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2254
R_work r_work	0.2236
R_free r_free	0.2589

Structure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of Rabenosyn-5

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

GTP-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

FYVE-finger-containing Rab5 effector protein rabenosyn-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

1z0k__assembly_2__model_1

1z0k__assembly_2__model_1 | I(q)

1z0k__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of Rabenosyn-5

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

GTP-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

FYVE-finger-containing Rab5 effector protein rabenosyn-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

1z0k__assembly_2__model_1

1z0k__assembly_2__model_1 | I(q)

1z0k__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)