4M22 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SMALL MOLECULE ACRYLAMIDE 16 COVALENTLY BOUND TO K-RAS G12C

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

Date :   05 Aug 13 (Deposition) - 27 Nov 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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 (3, 8)

No.	Name	Count	Type	Full Name
1	22C	2	Ligand/Ion	1-{4-[(2,4-DICHLOROPHENOXY)ACETYL]PIPERAZIN-1-YL}PROPAN-1-ONE
2	GDP	3	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	22C	-1	Ligand/Ion	1-{4-[(2,4-DICHLOROPHENOXY)ACETYL]PIPERAZIN-1-YL}PROPAN-1-ONE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	22C	1	Ligand/Ion	1-{4-[(2,4-DICHLOROPHENOXY)ACETYL]PIPERAZIN-1-YL}PROPAN-1-ONE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	22C	1	Ligand/Ion	1-{4-[(2,4-DICHLOROPHENOXY)ACETYL]PIPERAZIN-1-YL}PROPAN-1-ONE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:17 , GDP A:202 , HOH A:306 , HOH A:342 , HOH A:343 , HOH A:345	BINDING SITE FOR RESIDUE MG A 201
2	AC2	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 , TYR A:32 , 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:306 , HOH A:331 , HOH A:345	BINDING SITE FOR RESIDUE GDP A 202
3	AC3	SOFTWARE	SER B:17 , GDP B:203 , HOH B:302 , HOH B:305 , HOH B:361 , HOH B:363	BINDING SITE FOR RESIDUE MG B 201
4	AC4	SOFTWARE	CYS B:12 , LYS B:16 , PRO B:34 , ALA B:59 , GLY B:60 , GLN B:61 , GLU B:62 , GLU B:63 , ARG B:68 , TYR B:71 , MET B:72 , TYR B:96 , GDP B:203 , HOH B:303	BINDING SITE FOR RESIDUE 22C B 202
5	AC5	SOFTWARE	GLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , PHE B:28 , VAL B:29 , ASP B:30 , TYR B:32 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , MG B:201 , 22C B:202 , HOH B:302 , HOH B:313 , HOH B:315 , HOH B:317 , HOH B:329 , HOH B:361 , HOH B:363	BINDING SITE FOR RESIDUE GDP B 203
6	AC6	SOFTWARE	SER C:17 , GDP C:203 , HOH C:309 , HOH C:335 , HOH C:338 , HOH C:339	BINDING SITE FOR RESIDUE MG C 201
7	AC7	SOFTWARE	GLN B:70 , CYS C:12 , LYS C:16 , PRO C:34 , GLY C:60 , TYR C:71 , MET C:72 , TYR C:96 , GLN C:99 , GDP C:203 , HOH C:301	BINDING SITE FOR RESIDUE 22C C 202
8	AC8	SOFTWARE	GLY C:13 , VAL C:14 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , ASN C:116 , LYS C:117 , ASP C:119 , LEU C:120 , SER C:145 , ALA C:146 , LYS C:147 , MG C:201 , 22C C:202 , HOH C:313 , HOH C:315 , HOH C:316 , HOH C:317 , HOH C:335 , HOH C:338 , HOH C:339	BINDING SITE FOR RESIDUE GDP C 203

(no "SS Bond" information available for 4M22)

(no "Cis Peptide Bond" information available for 4M22)

(no "SAP(SNP)/Variant" information available for 4M22)

(no "PROSITE Motif" information available for 4M22)

(no "Exon" information available for 4M22)

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:160
                                                                                                                                                                                                
               SCOP domains d4m22a_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee...hhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m22 A   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTARDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        30        40        50        68        78        88        98       108       118       128       138       148       158       168
                                                                                     59|                                                                                                    
                                                                                      68

Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d4m22b_ B: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh...........eeeeeeee....eeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m22 B   2 TEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4m22c_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh.........eeeeeeee....eeeeeeee....hhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m22 C   2 TEYKLVVVGACGVGKSALTIQLIQNHFVDDPTIEDSYRKQVVIDGETSLLDILDTAGMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    11        21        33        43        53      ||69        79        89        99       109       119       129       139       149       159         
                                                       30|                         60|                                                                                                     
                                                        33                          67

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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

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Superfamilies( (-)

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Protein Domains( (-)

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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	d4m22a_	A:
1b	d4m22b_	B:
1c	d4m22c_	C:

(no "CATH Domain" information available for 4M22)

(no "Pfam Domain" information available for 4M22)

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	Cis Peptide Bonds
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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
4luc	RELATED COMPOUND BOUND TO PROTEIN
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

Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

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