5F2E - JenaLib

Title :   CRYSTAL STRUCTURE OF SMALL MOLECULE ARS-853 COVALENTLY BOUND TO K-RAS G12C

Authors :   M. P. Patricelli, M. R. Janes, L. -S. Li, R. Hansen, U. Peters, L. V. Kessl Y. Chen, J. M. Kucharski, J. Feng, T. Ely, J. H. Chen, S. J. Firdaus, A. Ba P. Ren, Y. Liu

Date :   01 Dec 15 (Deposition) - 13 Jan 16 (Release) - 16 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Small Gtpase Domain, Covalent Inhibitor Bound, Switch Ii Pocket, Gdp Bound, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. P. Patricelli, M. R. Janes, L. S. Li, R. Hansen, U. Peters, L. V. Kessler, Y. Chen, J. M. Kucharski, J. Feng, T. Ely, J. H. Chen, S. J. Firdaus, A. Babbar, P. Ren, Y. Liu
Selective Inhibition Of Oncogenic Kras Output With Small Molecules Targeting The Inactive State.
Cancer Discov V. 6 316 2016
PubMed-ID: 26739882 | Reference-DOI: 10.1158/2159-8290.CD-15-1105

Compounds

Molecule 1 - GTPASE KRAS
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJEXPRESS411
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	GTPASE DOMAIN
	Gene	:	KRAS, KRAS2, RASK2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:17 , GDP A:206 , HOH A:342 , HOH A:349 , HOH A:352 , HOH A:382	binding site for residue MG A 201
2	AC2	SOFTWARE	ASP A:47 , PHE A:90 , GLU A:91 , ILE A:93 , HIS A:94 , LEU A:133 , HOH A:309	binding site for residue GOL A 202
3	AC3	SOFTWARE	ARG A:97 , GLU A:107 , SER A:136 , TYR A:137 , ILE A:142 , GLU A:143 , GLY A:151 , ASP A:154	binding site for residue GOL A 203
4	AC4	SOFTWARE	VAL A:9 , GLY A:10 , CYS A:12 , LYS A:16 , PRO A:34 , ALA A:59 , GLY A:60 , GLU A:62 , GLU A:63 , TYR A:64 , ARG A:68 , ASP A:69 , MET A:72 , TYR A:96 , GLN A:99 , VAL A:103 , HOH A:314 , HOH A:352 , HOH A:407	binding site for residue 5UT A 204
5	AC5	SOFTWARE	TYR A:4 , GLU A:49 , ASN A:85 , LEU A:120 , PRO A:121 , SER A:122 , ARG A:164 , HOH A:313 , HOH A:317	binding site for residue GLY A 205
6	AC6	SOFTWARE	GLY A:0 , GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , ASP A:30 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , MG A:201 , HOH A:337 , HOH A:342 , HOH A:349 , HOH A:352 , HOH A:378 , HOH A:380 , HOH A:416 , HOH A:418	binding site for residue GDP A 206

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.......hhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f2e A   0 GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKG 205
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       ||
                                                                                                                                                                                                 167|
                                                                                                                                                                                                  205

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (49, 49)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		5UT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5f2e)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5f2e
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RASK_HUMAN \| P01116
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RASK_HUMAN \| P01116
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description