SAXSdb — 2odb

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

Human Cell Division Cycle 42 (CDC42)

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Serine/threonine-protein kinase PAK 6 × 1 （Q9NQU5） CHLORIDE ION × 1 MAGNESIUM ION × 1 SULFATE ION × 3 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Serine/threonine-protein kinase PAK 6 × 2 （Q9NQU5） CHLORIDE ION × 2 MAGNESIUM ION × 2 SULFATE ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Serine/threonine-protein kinase PAK 6 × 2 （Q9NQU5） CHLORIDE ION × 2 MAGNESIUM ION × 2 SULFATE ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Serine/threonine-protein kinase PAK 6 × 2 （Q9NQU5） CHLORIDE ION × 2 MAGNESIUM ION × 2 SULFATE ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDC42_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–182； UniProt 1–181

Serine/threonine-protein kinase PAK 6

OrganismNot specified

UniProt Q9NQU5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Human Cell Division Cycle 42 (CDC42) × 1 （P60953） CHLORIDE ION × 1 MAGNESIUM ION × 1 SULFATE ION × 3 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Human Cell Division Cycle 42 (CDC42) × 2 （P60953） CHLORIDE ION × 2 MAGNESIUM ION × 2 SULFATE ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Human Cell Division Cycle 42 (CDC42) × 2 （P60953） CHLORIDE ION × 2 MAGNESIUM ION × 2 SULFATE ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Human Cell Division Cycle 42 (CDC42) × 2 （P60953） CHLORIDE ION × 2 MAGNESIUM ION × 2 SULFATE ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAK6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–35； UniProt 11–45

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	2odb
Deposition date deposition_date	2006-12-22
Structure title title	The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)
Keywords keywords	small GTPase, CRIB, kinase, protein-protein complex, Structural Genomics, Structural Genomics Consortium, SGC, PROTEIN BINDING; PROTEIN BINDING
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.

2odb__assembly_1__model_1

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

Download this curve (.dat)

2odb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2odb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.08 Å
Rg (electron density)	16.89 Å
Total Rg	17.92 Å
Atom count	1674
Residues	212
Excluded volume	29765 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2odb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2odb__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2odb__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2odb__assembly_4__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	Human Cell Division Cycle 42 (CDC42)
Molecular weight formula_weight	21370.7 kDa
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	1719

SMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVLL

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein kinase PAK 6
Molecular weight formula_weight	4066.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EISAPQNFQHRVHTSFDPKEGKFVGLPPQWQNILD

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Molecular weight formula_weight	521.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2odba_
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 (1 domains)

Domain ID domain_id	2odbA00
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	162.366 Å
Unit-cell length b length_b	162.366 Å
Unit-cell length c length_c	45.968 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 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	40.590 Å
R factor r_factor	0.2048
R_work r_work	0.2034
R_free r_free	0.2318

The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)

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

Human Cell Division Cycle 42 (CDC42)

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein kinase PAK 6

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

2odb__assembly_1__model_1

2odb__assembly_1__model_1 | I(q)

2odb__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)

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

Human Cell Division Cycle 42 (CDC42)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein kinase PAK 6

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

2odb__assembly_1__model_1

2odb__assembly_1__model_1 | I(q)

2odb__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)