4M69 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE MOUSE RIP3-MLKL COMPLEX

Authors :   T. Xie, W. Peng, C. Yan, J. Wu, Y. Shi

Date :   09 Aug 13 (Deposition) - 16 Oct 13 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Kinase, Phosphorylation, Transferase-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Xie, W. Peng, C. Yan, J. Wu, X. Gong, Y. Shi
Structural Insights Into Rip3-Mediated Necroptotic Signalin
Cell Rep V. 5 70 2013
PubMed-ID: 24095729 | Reference-DOI: 10.1016/J.CELREP.2013.08.044

Molecule 1 - RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 3
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 1-313
	Gene	:	RIPK3
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	RIP-LIKE PROTEIN KINASE 3, RECEPTOR-INTERACTING PROTEIN 3, RIP-3, MRIP3

Molecule 2 - MIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 182-464
	Gene	:	MLKL
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 9)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CL	2	Ligand/Ion	CHLORIDE ION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	SEP	2	Mod. Amino Acid	PHOSPHOSERINE
5	SO4	2	Ligand/Ion	SULFATE ION
6	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:28 , GLY A:29 , LYS A:30 , GLY A:31 , GLY A:32 , PHE A:33 , GLY A:34 , VAL A:36 , ALA A:49 , LYS A:51 , THR A:95 , ARG A:96 , PHE A:97 , MET A:98 , SER A:102 , ASP A:143 , LYS A:145 , SER A:147 , ASN A:148 , LEU A:150 , ASP A:161 , MG A:403 , HOH A:526 , HOH A:551 , HOH A:574 , HOH A:583 , HOH A:584 , HOH A:594	BINDING SITE FOR RESIDUE ANP A 401
2	AC2	SOFTWARE	ARG A:69 , ASN A:70 , GLU A:71 , VAL A:73 , LEU A:75 , ARG A:96 , LYS A:158 , HOH A:528	BINDING SITE FOR RESIDUE SO4 A 402
3	AC3	SOFTWARE	ASN A:148 , ASP A:161 , ANP A:401 , HOH A:593	BINDING SITE FOR RESIDUE MG A 403
4	AC4	SOFTWARE	ASP A:86	BINDING SITE FOR RESIDUE CL A 404
5	AC5	SOFTWARE	ARG A:42	BINDING SITE FOR RESIDUE CL A 405
6	AC6	SOFTWARE	PRO B:215 , ARG B:301 , ARG B:304	BINDING SITE FOR RESIDUE SO4 B 501

(no "SS Bond" information available for 4M69)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:136	-	Pro A:137
2	Pro B:193	-	Pro B:194
3	Lys B:264	-	Pro B:265

(no "SAP(SNP)/Variant" information available for 4M69)

(no "PROSITE Motif" information available for 4M69)

(no "Exon" information available for 4M69)

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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh.eeeeeeeee...eeeeeeee....eeeeeeee.....hhhhhhhhhh.........ee...eee..eee.eeeee.....hhhhhh......hhhhhhhhhhhhhhhhhhhhhh.........hhh.eee.....eee...hhhhhh.hhhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.......hhhhh........hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m69 A  12 SAVPLVSREELKKLEFVGKGGFGVVFRAHHRTWNHDVAVKIVNSKKISWEVKAMVNLRNENVLLLLGVTEDLQWDFVSGQALVTRFMENGSLAGLLQPECPRPWPLLCRLLQEVVLGMCYLHSLDPPLLHRDLKPSNILLDPELHAKLADFGLSTFQDsGGTLAYLDPELLFKVNLKASKASDVYSFGILVWAVLAGREAELVDKtsLIRETVCDRQSRPPLTELPPGSPETPGLEKLKELMIHCWGSQSENRPSFQDCEPKTNEVYNLVKDKVDAAVSEVKHYLSQ 312
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      |185       195       205       215       225     ||235       245       255       265       275       285       295       305       
                                                                                                                                                                                      168||                                            231-TPO                                                                             
                                                                                                                                                                                       183|                                             232-SEP                                                                            
                                                                                                                                                                                        184-SEP

Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4m69b_ B: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh....eeeee...eeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeeeee......eeeeeee.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee.hhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m69 B 182 QIKEIPKEHLGPPWTKLKTSKMSTIYRGEYHRSPVTIKVFNNPQAESVGIVRFTFNDEIKTMKKFDSPNILRIFGICIDQTVKPPEFSIVMEYCELGTLRELLDREKDLTMSVRSLLVLRAARGLYRLHHSETLHRNISSSSFLVAGGYQVKLAGFELSKTQNSSSTIYVSPERLKNPFCLYDIKAEIYSFGIVLWEIATGKIPFEGCDSKKIRELVAEDKKQEPVGQDCPELLREIINECRAHEPSQRPSVDGILERLSAVEE 458
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341  ||   364       374       384       394       404       414       424       434       444       454    
                                                                                                                                                                                            344|                                                                                                    
                                                                                                                                                                                             358

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( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: automated matches (529)

Protein domain: automated matches (529)

Mouse (Mus musculus) [TaxId: 10090] (14)

d4m69b_

(no "CATH Domain" information available for 4M69)

(no "Pfam Domain" information available for 4M69)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		ANP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SEP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		TPO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:136 - Pro A:137	[ RasMol ]
		Lys B:264 - Pro B:265	[ RasMol ]
		Pro B:193 - Pro B:194	[ RasMol ]

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Access by PDB/NDB ID
	4m69
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	MLKL_MOUSE \| Q9D2Y4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RIPK3_MOUSE \| Q9QZL0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.11.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
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Access by UniProt ID/Accession number
	MLKL_MOUSE \| Q9D2Y4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RIPK3_MOUSE \| Q9QZL0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MLKL_MOUSE \| Q9D2Y4	:	4btf 4m68
	RIPK3_MOUSE \| Q9QZL0	:	4m66

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 9)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (51, 61)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File