4LPK - JenaLib

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Title :   CRYSTAL STRUCTURE OF K-RAS WT, GDP-BOUND

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

Date :   16 Jul 13 (Deposition) - 27 Nov 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Gtpase, Gdp Bound, Signaling Protein (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 Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

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 , CA A:202 , HOH A:302 , HOH A:315 , HOH A:322 , HOH A:341 , HOH A:353 , HOH A:392	BINDING SITE FOR RESIDUE GDP A 201
2	AC2	SOFTWARE	SER A:17 , GDP A:201 , HOH A:302 , HOH A:305 , HOH A:306 , HOH A:322	BINDING SITE FOR RESIDUE CA A 202
3	AC3	SOFTWARE	GLU A:37 , ALA A:59 , HOH A:321 , HOH A:328 , HOH A:363	BINDING SITE FOR RESIDUE NA A 203
4	AC4	SOFTWARE	GLY B:12 , 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 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , CA B:202 , HOH B:307 , HOH B:312 , HOH B:313 , HOH B:349 , HOH B:361 , HOH B:367 , HOH B:379	BINDING SITE FOR RESIDUE GDP B 201
5	AC5	SOFTWARE	SER B:17 , GDP B:201 , HOH B:307 , HOH B:309 , HOH B:310 , HOH B:312	BINDING SITE FOR RESIDUE CA B 202
6	AC6	SOFTWARE	HOH B:337 , HOH B:370	BINDING SITE FOR RESIDUE NA B 203

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

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

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

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

(no "Exon" information available for 4LPK)

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
	(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:156
                                                                                                                                                                                            
               SCOP domains d4lpka_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.........eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lpk A   1 MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKH 166
                                    10        20        30        40        50        60|       80        90       100       110       120       130       140       150       160      
                                                                                      60|                                                                                               
                                                                                       71

Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d4lpkb_ 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.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lpk B   1 MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKH 166
                                    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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

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	d4lpka_	A:
1b	d4lpkb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
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		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ 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 4lpk)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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		Orientation in Membranes	:	OPM
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	RASK_HUMAN \| P01116
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4l8g	RELATED MUTANT OF PROTEIN
4l9s	MUTANT IN RELATED PROTEIN
4l9w	MUTANT IN RELATED 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
4m22	RELATED COMPOUND BOUND TO PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

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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