SAXSdb — 9i7y

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

Isoform 2B of GTPase KRas

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] (3~{S})-3-(propanoylamino)piperidine-1-carboxylate ; × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] (3~{S})-3-(propanoylamino)piperidine-1-carboxylate ; × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] (3~{S})-3-(propanoylamino)piperidine-1-carboxylate ; × 1 MAGNESIUM ION × 1 water × 1	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 3–171； UniProt 1–169 Author chain B； PDBConstruct 3–171； UniProt 1–169 Author chain C； PDBConstruct 3–171； UniProt 1–169

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	9i7y
Deposition date deposition_date	2025-02-03
Last revision last_revision	2025-11-12
Structure title title	Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor 7b
Keywords keywords	KRas, GTPase, Nucleotide-based Inhibitor, covalent, G13C, HYDROLASE; HYDROLASE
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.

9i7y__assembly_2__model_1

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

Download this curve (.dat)

9i7y__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9i7y__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.07 Å
Rg (electron density)	14.65 Å
Total Rg	15.73 Å
Atom count	1281
Residues	161
Excluded volume	22408 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9i7y__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9i7y__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9i7y__assembly_3__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Isoform 2B of GTPase KRas
Molecular weight formula_weight	19490.9 kDa
EC 编号 ec_number	3.6.5.2
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	3890

GHMTEYKLVVVGAGCVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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 non-polymer

Description description	;[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] (3~{S})-3-(propanoylamino)piperidine-1-carboxylate ;
Molecular weight formula_weight	625.4 kDa
Source method src_method	syn
Copy count entity_count	3

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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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Unit-cell length a length_a	70.010 Å
Unit-cell length b length_b	84.760 Å
Unit-cell length c length_c	88.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	42.380 Å
R factor r_factor	0.1917
R_work r_work	0.1898
R_free r_free	0.2278

Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor 7b

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

Isoform 2B of GTPase KRas

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

9i7y__assembly_2__model_1

9i7y__assembly_2__model_1 | I(q)

9i7y__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 (4)

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 water

7. Citations (1)

Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor 7b

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

Isoform 2B of 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9i7y__assembly_2__model_1

9i7y__assembly_2__model_1 | I(q)

9i7y__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 (4)

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 water

7. Citations (1)