SAXSdb — 4cym

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

RAS-RELATED PROTEIN RAB-32

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	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 × 2 （Q96NW4） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 × 2 （Q96NW4） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 × 2 （Q96NW4） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 × 1 （Q96NW4） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 × 1 （Q96NW4） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 × 1 （Q96NW4） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB32_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–230； UniProt 1–225 Author chain B； PDBConstruct 6–230； UniProt 1–225 Author chain C； PDBConstruct 6–230； UniProt 1–225

ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27

HOMO SAPIENS

UniProt Q96NW4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RAS-RELATED PROTEIN RAB-32 × 2 （Q13637） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	RAS-RELATED PROTEIN RAB-32 × 2 （Q13637） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	RAS-RELATED PROTEIN RAB-32 × 2 （Q13637） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	RAS-RELATED PROTEIN RAB-32 × 1 （Q13637） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	RAS-RELATED PROTEIN RAB-32 × 1 （Q13637） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	RAS-RELATED PROTEIN RAB-32 × 1 （Q13637） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ANR27_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 7–197； UniProt 450–640 Author chain E； PDBConstruct 7–197； UniProt 450–640 Author chain F； PDBConstruct 7–197； UniProt 450–640

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	4cym
Deposition date deposition_date	2014-04-13
Structure title title	Complex of human VARP-ANKRD1 with Rab32-GppCp
Keywords keywords	TRANSPORT PROTEIN, VARP, RAB-EFFECTOR, RAB, ENDOSOME, VESICLE TRAFFICKING, MELANOSOME BIOGENESIS; TRANSPORT 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.

4cym__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4cym__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4cym__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	22.68 Å
Rg (electron density)	21.57 Å
Total Rg	22.41 Å
Atom count	2697
Residues	340
Excluded volume	47858 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4cym__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4cym__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4cym__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4cym__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4cym__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4cym__assembly_6__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-32
Molecular weight formula_weight	25425.8 kDa
EC 编号 ec_number	3.6.5.2
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8282

GPLGSMAGGGAGDPGLGAAAAPAPETREHLFKVLVIGELGVGKTSIIKRYVHQLFSQHYRATIGVDFALKVLNWDSRTLVRLQLWDIAGLERFGNMTRVYYKEAVGAFVVFDISRSSTFEAVLKWKSDLDSKVHLPNGSPIPAVLLANKCDQNKDSSQSPSQVDQFCKEHGFAGWFETSAKDNINIEEAARFLVEKILVNHQSFPNEENDVDKIKLDQETLRAENKSQCC

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	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
Molecular weight formula_weight	22312.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

GPLGSMDPSVVTPFSRDDRGHTPLHVAAVCGQASLIDLLVSKGAMVNATDYHGATPLHLACQKGYQSVTLLLLHYKASAEVQDNNGNTPLHLACTYGHEDCVKALVYYDVESCRLDIGNEKGDTPLHIAARWGYQGVIETLLQNGASTEIQNRLKETPLKCALNSKILSVMEAYHLSFERRQKSSEAPVQSPQRSVDHHHHHH

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	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Molecular weight formula_weight	521.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
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	131

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4cyma_
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	d4cymb_
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	d4cymc_
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 (6 domains)

Domain ID domain_id	4cymA00
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	4cymB00
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	4cymC00
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	4cymD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	4cymE00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	4cymF00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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Unit-cell length a length_a	144.445 Å
Unit-cell length b length_b	144.445 Å
Unit-cell length c length_c	135.680 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	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	125.090 Å
R factor r_factor	0.1947
R_work r_work	0.1920
R_free r_free	0.2457

Complex of human VARP-ANKRD1 with Rab32-GppCp

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

RAS-RELATED PROTEIN RAB-32

State in the Current Structure

Other States of the Same Protein in the Database

ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27

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

4cym__assembly_5__model_1

4cym__assembly_5__model_1 | I(q)

4cym__assembly_5__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Complex of human VARP-ANKRD1 with Rab32-GppCp

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

RAS-RELATED PROTEIN RAB-32

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27

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

4cym__assembly_5__model_1

4cym__assembly_5__model_1 | I(q)

4cym__assembly_5__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)