9BI1

Crystal structure of GMPPNP bound KRAS G12D in complex with CYPA and RMC-7977

PDB DOI: https://doi.org/10.2210/pdb9BI1/pdb

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

Deposited: 2024-04-22 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: 0.260
R-Value Work: 0.218
R-Value Observed: 0.220

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of GMPPNP bound KRAS G12D in complex with CYPA and RMC-7977

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

To be published.

Macromolecule Content

Total Structure Weight: 77.78 kDa
Atom Count: 6,003
Modelled Residue Count: 664
Deposited Residue Count: 672
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, D [auth C]	170	Homo sapiens	Mutation(s): 1 Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116 Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	B, C [auth D]	166	Homo sapiens	Mutation(s): 0 Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937 Go to UniProtKB: P62937
PHAROS: P62937 GTEx: ENSG00000196262
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62937
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 G [auth B] SDF format, chain H [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth D]	G [auth B], H [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 G [auth B] Focus chain H [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth D]
GNP (Subject of Investigation/LOI) Query on GNP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C]	E [auth A], I [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C]	F [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]