4M21 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SMALL MOLECULE ACRYLAMIDE 11 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 :   1.94

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	21Y	1	Ligand/Ion	1-(4-{[(4,5-DICHLORO-2-METHOXYPHENYL)AMINO]ACETYL}PIPERAZIN-1-YL)PROPAN-1-ONE
2	GDP	3	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	21Y	-1	Ligand/Ion	1-(4-{[(4,5-DICHLORO-2-METHOXYPHENYL)AMINO]ACETYL}PIPERAZIN-1-YL)PROPAN-1-ONE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	21Y	1	Ligand/Ion	1-(4-{[(4,5-DICHLORO-2-METHOXYPHENYL)AMINO]ACETYL}PIPERAZIN-1-YL)PROPAN-1-ONE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	21Y	-1	Ligand/Ion	1-(4-{[(4,5-DICHLORO-2-METHOXYPHENYL)AMINO]ACETYL}PIPERAZIN-1-YL)PROPAN-1-ONE
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 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , HOH A:311 , HOH A:337 , HOH A:339 , HOH A:344	BINDING SITE FOR RESIDUE GDP A 201
2	AC2	SOFTWARE	VAL B:9 , GLY B:10 , CYS B:12 , THR B:58 , ARG B:68 , MET B:72 , TYR B:96 , GLN B:99	BINDING SITE FOR RESIDUE 21Y 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:319	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 , LEU C:120 , SER C:145 , ALA C:146 , LYS C:147	BINDING SITE FOR RESIDUE GDP C 201

(no "SS Bond" information available for 4M21)

(no "Cis Peptide Bond" information available for 4M21)

(no "SAP(SNP)/Variant" information available for 4M21)

(no "PROSITE Motif" information available for 4M21)

(no "Exon" information available for 4M21)

Asymmetric Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4m21a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh.......eeeeeeee..eeeeeeeeee....hhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m21 A   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDIEDSYRKQVVIDGETSLLDILDTAGQSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                    10        20        30|       45        55     || 68        78        88        98       108       118       128       138       148       158         
                                                        30|                       61|                                                                                                      
                                                         36                        65

Chain B from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains d4m21b_ B: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh......eeeeee..eeeeeee.....hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m21 B   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDSYRKQVVIDGETSLLDILDTAYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        38        48        58||      72        82        92       102       112       122       132       142       152       162      
                                                       29|                   59|                                                                                                        
                                                        38                    64

Chain C from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains d4m21c_ C: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh...eeee......eeeeeee...hhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m21 C   2 TEYKLVVVGACGVGKSALTIQLIQNHFYRKQVVIDGETSLLDILDTADQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                    11        21      ||42        52      ||71        81        91       101       111       121       131       141       151       161      
                                                     28|                 59|                                                                                                  
                                                      40                  69

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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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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	d4m21a_	A:
1b	d4m21b_	B:
1c	d4m21c_	C:

(no "CATH Domain" information available for 4M21)

(no "Pfam Domain" information available for 4M21)

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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		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 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
4m1y	PROTEIN BOUND TO RELATED COMPOUND
4m22	RELATED COMPOUND BOUND TO PROTEIN

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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