9bg4

Tri-complex of Compound-2, KRAS G12V, and CypA

Method: X-RAY DIFFRACTION

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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 4	Peptidyl-prolyl cis-trans isomerase A × 2 （P62937） PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 ;(2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) ; × 2 water × 4	Review required
2	Protein heterocomplex	Heteromer	Protein 4	Peptidyl-prolyl cis-trans isomerase A × 2 （P62937） PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 ;(2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) ; × 2 water × 4	Review required

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 2–170； UniProt 1–169 Author chain B； PDBConstruct 2–170； UniProt 1–169

Peptidyl-prolyl cis-trans isomerase A

Homo sapiens

UniProt P62937

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	GTPase KRas × 2 （P01116） PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 ;(2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) ; × 2 water × 4	Review required
2	Protein heterocomplex	Heteromer	Protein 4	GTPase KRas × 2 （P01116） PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 ;(2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) ; × 2 water × 4	Review required

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPIA_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–166； UniProt 1–165 Author chain D； PDBConstruct 2–166； UniProt 1–165

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	9bg4
Deposition date deposition_date	2024-04-18
Structure title title	Tri-complex of Compound-2, KRAS G12V, and CypA
Keywords keywords	inhibitor, complex, small GTPase, cancer, tricomplex, SIGNALING PROTEIN-INHIBITOR complex, SIGNALING PROTEIN; SIGNALING PROTEIN/INHIBITOR
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.

9bg4__assembly_1__model_1

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

Download this curve (.dat)

9bg4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bg4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.56 Å
Rg (electron density)	27.88 Å
Total Rg	28.63 Å
Atom count	5440
Residues	671
Excluded volume	95740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bg4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9bg4__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 (7)

Entity 1 Entity 1 polymer

Description description	GTPase KRas
Molecular weight formula_weight	19400.9 kDa
EC 编号 ec_number	3.6.5.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6735

SMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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	Peptidyl-prolyl cis-trans isomerase A
Molecular weight formula_weight	18123.6 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

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	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	;(2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) ;
Molecular weight formula_weight	779.0 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1057

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Unit-cell length a length_a	48.140 Å
Unit-cell length b length_b	101.630 Å
Unit-cell length c length_c	66.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.94 °
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	monoclinic

Resolution resolution	1.140 Å
Low-resolution limit resolution_low	55.480 Å
R factor r_factor	0.1425
R_work r_work	0.1407
R_free r_free	0.1772

Tri-complex of Compound-2, KRAS G12V, and CypA

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

Peptidyl-prolyl cis-trans isomerase A

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

9bg4__assembly_1__model_1

9bg4__assembly_1__model_1 | I(q)

9bg4__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

Source Source

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

7. Citations (1)

Tri-complex of Compound-2, KRAS G12V, and CypA

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

Peptidyl-prolyl cis-trans isomerase A

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

9bg4__assembly_1__model_1

9bg4__assembly_1__model_1 | I(q)

9bg4__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

Source Source

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

7. Citations (1)