3GFT | pdb_00003gft

Human K-Ras (Q61H) in complex with a GTP analogue

PDB DOI: https://doi.org/10.2210/pdb3GFT/pdb
Entry: 3GFT supersedes: 2PMX

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-27 Released: 2009-03-10
Deposition Author(s): Tong, Y., Tempel, W., Shen, L., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.267 (Depositor), 0.264 (DCC)
R-Value Work:
0.213 (Depositor), 0.214 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Human K-Ras in complex with a GTP analogue

Tong, Y., Tempel, W., Shen, L., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 132.36 kDa
Atom Count: 8,086
Modeled Residue Count: 966
Deposited Residue Count: 1,122
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, B, C, D, E A, B, C, D, E, F	187	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F]	H [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] H [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain T [auth F] MOL2 format, chain T [auth F] mmCIF format, chain T [auth F]	T [auth F]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain T [auth F] Interactions & Density Focus chain T [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F]	G [auth A] J [auth B] L [auth C] N [auth D] P [auth E] G [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.267 (Depositor), 0.264 (DCC)
R-Value Work: 0.213 (Depositor), 0.214 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.535	α = 90
b = 118.275	β = 90
c = 156.836	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 2PMX

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-09-05
Changes: Derived calculations
Version 1.3: 2015-01-28
Changes: Structure summary
Version 1.4: 2017-11-01
Changes: Advisory, Refinement description
Version 1.5: 2023-09-06
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description