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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SMALL MOLECULE DISULFIDE 6 BOUND TO K-RAS G12C

Authors :   J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat

Date :   25 Jul 13 (Deposition) - 27 Nov 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.29

Chains :   Asym./Biol. Unit : A,B

Keywords :   Gtpase, Gdp Bound, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat
K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity And Effector Interactions.
Nature V. 503 548 2013
PubMed-ID: 24256730 | Reference-DOI: 10.1038/NATURE12796

Molecule 1 - GTPASE KRAS
	Chains	:	A, B
	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	:	UNP RESIDUES 1-169
	Gene	:	KRAS, KRAS ISOFORM 2B, KRAS2, RASK2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	K-RAS 2, KI-RAS, C-K-RAS, C-KI-RAS, GTPASE KRAS, N- TERMINALLY PROCESSED

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	20G	2	Ligand/Ion	N-{1-[(2,4-DICHLOROPHENOXY)ACETYL]PIPERIDIN-4-YL}-4-SULFANYLBUTANAMIDE
2	CA	4	Ligand/Ion	CALCIUM ION
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:17 , GDP A:204 , HOH A:303 , HOH A:305 , HOH A:307 , HOH A:308	BINDING SITE FOR RESIDUE CA A 201
2	AC2	SOFTWARE	GLU A:63 , GLY A:138 , HOH A:306 , HOH A:318 , HOH A:320 , HOH A:346	BINDING SITE FOR RESIDUE CA A 202
3	AC3	SOFTWARE	VAL A:9 , GLY A:10 , CYS A:12 , GLY A:60 , GLN A:61 , GLU A:62 , ARG A:68 , TYR A:71 , MET A:72 , TYR A:96 , GLN A:99 , ILE A:100 , HOH A:324	BINDING SITE FOR RESIDUE 20G A 203
4	AC4	SOFTWARE	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 , ARG A:73 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , CA A:201 , HOH A:303 , HOH A:308 , HOH A:334 , HOH A:380 , HOH A:386 , HOH A:397 , HOH A:402 , HOH A:453	BINDING SITE FOR RESIDUE GDP A 204
5	AC5	SOFTWARE	SER B:17 , GDP B:204 , HOH B:302 , HOH B:306 , HOH B:308 , HOH B:309	BINDING SITE FOR RESIDUE CA B 201
6	AC6	SOFTWARE	GLU B:63 , GLY B:138 , HOH B:311 , HOH B:312 , HOH B:313 , HOH B:394	BINDING SITE FOR RESIDUE CA B 202
7	AC7	SOFTWARE	VAL B:9 , GLY B:10 , CYS B:12 , GLY B:60 , GLN B:61 , GLU B:62 , ARG B:68 , TYR B:71 , MET B:72 , TYR B:96 , GLN B:99 , ILE B:100 , HOH B:336	BINDING SITE FOR RESIDUE 20G B 203
8	AC8	SOFTWARE	GLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , ASP B:30 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , CA B:201 , HOH B:302 , HOH B:309 , HOH B:310 , HOH B:329 , HOH B:335 , HOH B:358 , HOH B:366	BINDING SITE FOR RESIDUE GDP B 204

(no "SS Bond" information available for 4LUC)

(no "Cis Peptide Bond" information available for 4LUC)

(no "SAP(SNP)/Variant" information available for 4LUC)

(no "PROSITE Motif" information available for 4LUC)

(no "Exon" information available for 4LUC)

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:168
                                                                                                                                                                                                        
               SCOP domains d4luca_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4luc A   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains d4lucb_ B: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4luc B   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: automated matches (173)

Human (Homo sapiens) [TaxId: 9606] (112)

1a	d4luca_	A:
1b	d4lucb_	B:

(no "CATH Domain" information available for 4LUC)

(no "Pfam Domain" information available for 4LUC)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4luc)

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	4luc
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		Orientation in Membranes	:	OPM
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4l8g	RELATED MUTANT OF PROTEIN
4l9s	MUTANT IN RELATED PROTEIN
4l9w	MUTANT IN RELATED PROTEIN
4lpk	WILD-TYPE PROTEIN
4lrw	PROTEIN WITHOUT COMPOUND BOUND
4lv6	RELATED COMPOUND BOUND TO PROTEIN
4lyf	RELATED COMPOUND BOUND TO PROTEIN
4lyh	RELATED COMPOUND BOUND TO PROTEIN
4lyj	RELATED COMPOUND BOUND TO PROTEIN
4m1o	RELATED COMPOUND BOUND TO PROTEIN
4m1s	RELATED COMPOUND BOUND TO PROTEIN
4m1t	RELATED COMPOUND BOUND TO PROTEIN
4m1w	RELATED COMPOUND BOUND TO PROTEIN
4m1y	RELATED COMPOUND BOUND TO PROTEIN
4m21	RELATED COMPOUND BOUND TO PROTEIN
4m22	RELATED COMPOUND BOUND TO PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (49, 49)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File