SAXSdb — 5tb5

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

GTPase KRas

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	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ; × 1 （O43924） FARNESYL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ; × 1 （O43924） FARNESYL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RASK_HUMAN
Isoform	P01116-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–185； UniProt 2–185 Author chain C； PDBConstruct 2–185； UniProt 2–185

;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ;

Homo sapiens

UniProt O43924

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GTPase KRas × 1 （P01116） FARNESYL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	GTPase KRas × 1 （P01116） FARNESYL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDE6D_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–150； UniProt 1–150 Author chain D； PDBConstruct 1–150； UniProt 1–150

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	5tb5
Deposition date deposition_date	2016-09-11
Structure title title	Crystal structure of full-length farnesylated and methylated KRAS4b in complex with PDE-delta (crystal form I - with partially disordered hypervariable region)
Keywords keywords	KRAS4b, PDEdelta, PDE6delta, RAS, KRAS, ONCOPROTEIN; ONCOPROTEIN
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.

5tb5__assembly_1__model_1

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

Download this curve (.dat)

5tb5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tb5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.03 Å
Rg (electron density)	28.43 Å
Total Rg	29.18 Å
Atom count	2638
Residues	322
Excluded volume	47007 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tb5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5tb5__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	GTPase KRas
Molecular weight formula_weight	21056.0 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	5416

GTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKC

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	unidentified baculovirus

Entity 2 Entity 2 polymer

Description description	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ;
Molecular weight formula_weight	17441.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

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	FARNESYL
Molecular weight formula_weight	206.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	160

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5tb5b_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.8 — RhoGDI-like

Domain ID domain_id	d5tb5d_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.8 — RhoGDI-like

CATH v4.4 (4 domains)

Domain ID domain_id	5tb5A00
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	5tb5B00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	50 — Coagulation Factor XIII; Chain A, domain 1
Homologous superfamily homologous superfamily	40 — GMP phosphodiesterase, delta subunit

Domain ID domain_id	5tb5C00
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	5tb5D00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	50 — Coagulation Factor XIII; Chain A, domain 1
Homologous superfamily homologous superfamily	40 — GMP phosphodiesterase, delta subunit

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Unit-cell length a length_a	58.386 Å
Unit-cell length b length_b	70.651 Å
Unit-cell length c length_c	94.307 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	48.695 Å
R factor r_factor	0.2054
R_work r_work	0.2007
R_free r_free	0.2476

Crystal structure of full-length farnesylated and methylated KRAS4b in complex with PDE-delta (crystal form I - with partially disordered hypervariable region)

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

GTPase KRas

State in the Current Structure

Other States of the Same Protein in the Database

;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ;

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

5tb5__assembly_1__model_1

5tb5__assembly_1__model_1 | I(q)

5tb5__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of full-length farnesylated and methylated KRAS4b in complex with PDE-delta (crystal form I - with partially disordered hypervariable region)

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

GTPase KRas

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ;

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

5tb5__assembly_1__model_1

5tb5__assembly_1__model_1 | I(q)

5tb5__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)