SAXSdb — 9usb

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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	MAGNESIUM ION × 1 ;(3~{R})-1-[2-[[(8~{S})-6-[bis(fluoranyl)methylidene]-2,3,5,7-tetrahydro-1~{H}-pyrrolizin-8-yl]methoxy]-7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-pyrido[4,3-d]pyrimidin-4-yl]-3-methyl-piperidin-3-ol ; × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 ;(3~{R})-1-[2-[[(8~{S})-6-[bis(fluoranyl)methylidene]-2,3,5,7-tetrahydro-1~{H}-pyrrolizin-8-yl]methoxy]-7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-pyrido[4,3-d]pyrimidin-4-yl]-3-methyl-piperidin-3-ol ; × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 ;(3~{R})-1-[2-[[(8~{S})-6-[bis(fluoranyl)methylidene]-2,3,5,7-tetrahydro-1~{H}-pyrrolizin-8-yl]methoxy]-7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-pyrido[4,3-d]pyrimidin-4-yl]-3-methyl-piperidin-3-ol ; × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 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 7–175； UniProt 1–169 Author chain B； PDBConstruct 7–175； UniProt 1–169 Author chain C； PDBConstruct 7–175； 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	9usb
Deposition date deposition_date	2025-05-01
Structure title title	GppNHp-bound KRAS G12D in complex with MCB-294
Keywords keywords	GppNHp-bound, inhibitor, 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.

9usb__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9usb__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9usb__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	16.35 Å
Rg (electron density)	15.09 Å
Total Rg	16.16 Å
Atom count	1438
Residues	170
Excluded volume	25142 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9usb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9usb__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9usb__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 (5)

Entity 1 Entity 1 polymer

Description description	Isoform 2B of GTPase KRas
Molecular weight formula_weight	19714.2 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	4308

GAGAGAMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	;(3~{R})-1-[2-[[(8~{S})-6-[bis(fluoranyl)methylidene]-2,3,5,7-tetrahydro-1~{H}-pyrrolizin-8-yl]methoxy]-7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-pyrido[4,3-d]pyrimidin-4-yl]-3-methyl-piperidin-3-ol ;
Molecular weight formula_weight	633.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 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	74

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Unit-cell length a length_a	47.184 Å
Unit-cell length b length_b	102.574 Å
Unit-cell length c length_c	56.362 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	23.810 Å
R factor r_factor	0.1763
R_work r_work	0.1730
R_free r_free	0.2423

GppNHp-bound KRAS G12D in complex with MCB-294

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

9usb__assembly_3__model_1

9usb__assembly_3__model_1 | I(q)

9usb__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

GppNHp-bound KRAS G12D in complex with MCB-294

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

9usb__assembly_3__model_1

9usb__assembly_3__model_1 | I(q)

9usb__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)