9BGH

Crystal structure of KRAS G12D in a transition state mimetic complex with CYPA and RMC-7977

PDB DOI: https://doi.org/10.2210/pdb9BGH/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes mpstruc

Deposited: 2024-04-18 Released: 2024-11-06
Deposition Author(s): Pourfarjam, Y., Goldgur, Y., Cuevas-Navarro, A., Lito, P.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.251
R-Value Work: 0.218
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of KRAS G12D in a transition state mimetic complex with CYPA and RMC-7977

Pourfarjam, Y., Goldgur, Y., Cuevas-Navarro, A., Lito, P.

To be published.

Macromolecule Content

Total Structure Weight: 77.71 kDa
Atom Count: 5,837
Modelled Residue Count: 663
Deposited Residue Count: 672
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A [auth B], B [auth D]	166	Homo sapiens	Mutation(s): 0 Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt
Find proteins for P62938 (Chlorocebus aethiops) Explore P62938 Go to UniProtKB: P62938
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62938
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	C [auth A], D [auth C]	170	Homo sapiens	Mutation(s): 1 Gene Names: KRAS EC: 3.6.5.2 Membrane Entity: Yes
UniProt
Find proteins for P79800 (Meleagris gallopavo) Explore P79800 Go to UniProtKB: P79800
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P79800
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZNI (Subject of Investigation/LOI) Query on ZNI Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth D] mmCIF format, chain E [auth B] mmCIF format, chain F [auth D]	E [auth B], F [auth D]	(1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide C₄₇ H₆₀ N₈ O₆ S NBLZKEHVVJSAAY-VLXWOFRQSA-N		Interactions Focus chain E [auth B] Focus chain F [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth D]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C]	G [auth A], I [auth C]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain I [auth C] Interactions & Density Focus chain G [auth A] Focus chain I [auth C]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth C]	H [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth C]