4M1Y - JenaLib

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Title :   CRYSTAL STRUCTURE OF SMALL MOLECULE VINYLSULFONAMIDE 15 COVALENTLY BOUND TO K-RAS G12C

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

Date :   04 Aug 13 (Deposition) - 27 Nov 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Gtpase, Gdp Bound, Small Molecule Inhibitor, Covalent Binder, 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 - K-RAS GTPASE
	Chains	:	A, B, C
	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	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	21S	1	Ligand/Ion	N-{1-[N-(5,7-DICHLORO-2,1,3-BENZOTHIADIAZOL-4-YL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2	GDP	3	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	21S	-1	Ligand/Ion	N-{1-[N-(5,7-DICHLORO-2,1,3-BENZOTHIADIAZOL-4-YL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	21S	1	Ligand/Ion	N-{1-[N-(5,7-DICHLORO-2,1,3-BENZOTHIADIAZOL-4-YL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	21S	-1	Ligand/Ion	N-{1-[N-(5,7-DICHLORO-2,1,3-BENZOTHIADIAZOL-4-YL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	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 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , HOH A:324 , HOH A:331 , HOH A:343 , HOH A:345 , HOH A:357 , HOH A:359 , HOH A:361 , HOH A:400 , HOH A:403 , HOH A:430	BINDING SITE FOR RESIDUE GDP A 201
2	AC2	SOFTWARE	VAL B:8 , VAL B:9 , GLY B:10 , CYS B:12 , THR B:58 , GLU B:62 , ARG B:68 , TYR B:71 , TYR B:96 , GLN B:99	BINDING SITE FOR RESIDUE 21S B 201
3	AC3	SOFTWARE	GLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , PHE B:28 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , HOH B:353 , HOH B:364 , HOH B:369 , HOH B:397 , HOH B:406 , HOH B:409 , HOH B:410 , HOH B:412	BINDING SITE FOR RESIDUE GDP B 202
4	AC4	SOFTWARE	GLY C:13 , VAL C:14 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , ALA C:59 , ASN C:116 , LYS C:117 , ASP C:119 , SER C:145 , ALA C:146 , LYS C:147 , HOH C:311 , HOH C:327	BINDING SITE FOR RESIDUE GDP C 201

(no "SS Bond" information available for 4M1Y)

(no "Cis Peptide Bond" information available for 4M1Y)

(no "SAP(SNP)/Variant" information available for 4M1Y)

(no "PROSITE Motif" information available for 4M1Y)

(no "Exon" information available for 4M1Y)

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains d4m1ya_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh.......eeeeeeee..eeeeeeeeee....hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m1y A   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDEEDSYRKQVVIDGETSLLDILDTAGEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        30||      45        55    ||  66        76        86        96       106       116       126       136       146       156       166  
                                                         31|                     60|                                                                                                          
                                                          37                      62

Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains d4m1yb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh......eeeeee..eeeeeee........hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m1y B   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK 169
                                    10        20        38        48        58        68        78        88        98       108       118       128       138       148       158       168 
                                                       29|                                                                                                                                   
                                                        38

Chain C from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4m1yc_ C: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh....eeeeeee..eeeeeeeee....hhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m1y C   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVSYRKQVVIDGETSLLDILDTAGRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                    10        20        39        49        59||      76        86        96       106       116       126       136       146       156       166 
                                                       29|                   60|                                                                                                   
                                                        39                    68

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	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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

)

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	d4m1ya_	A:
1b	d4m1yb_	B:
1c	d4m1yc_	C:

(no "CATH Domain" information available for 4M1Y)

(no "Pfam Domain" information available for 4M1Y)

Asymmetric Unit(hide GO term definitions)

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Biological Units
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		Biological Unit 1	[ Jena3D ]
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		Biological Unit 3	[ Jena3D ]

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4l8g	RELATED MUTANT OF PROTEIN
4l9s	MUTANT IN RELATED PROTEIN
4l9w	MUTANT IN RELATED PROTEIN
4lpk	WILD-TYPE OF PROTEIN
4lrw	PROTEIN WITHOUT SMALL MOLECULE BOUND
4luc	PROTEIN BOUND TO RELATED COMPOUND
4lv6	PROTEIN BOUND TO RELATED COMPOUND
4lyf	PROTEIN BOUND TO RELATED COMPOUND
4lyh	PROTEIN BOUND TO RELATED COMPOUND
4lyj	PROTEIN BOUND TO RELATED COMPOUND
4m1o	PROTEIN BOUND TO RELATED COMPOUND
4m1s	PROTEIN BOUND TO RELATED COMPOUND
4m1t	PROTEIN BOUND TO RELATED COMPOUND
4m1w	PROTEIN BOUND TO RELATED COMPOUND
4m21	RELATED COMPOUND BOUND TO PROTEIN
4m22	RELATED COMPOUND BOUND TO PROTEIN

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 3)

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Gene Ontology (49, 49)

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