5HVK - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LIMK1 MUTANT D460N IN COMPLEX WITH FULL-LENGTH COFILIN-1

Authors :   S. Hamill, T. J. Boggon

Date :   28 Jan 16 (Deposition) - 04 May 16 (Release) - 18 May 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

Keywords :   Kinase Substrate Actin-Remodeling, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Hamill, H. J. Lou, B. E. Turk, T. J. Boggon
Structural Basis For Noncanonical Substrate Recognition Of Cofilin/Adf Proteins By Lim Kinases.
Mol. Cell V. 62 397 2016
PubMed-ID: 27153537 | Reference-DOI: 10.1016/J.MOLCEL.2016.04.001

Molecule 1 - LIM DOMAIN KINASE 1
	Chains	:	A, C
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	PFASTBAC HTB
	Fragment	:	UNP RESIDUES 329-638
	Gene	:	LIMK1, LIMK
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LIMK-1

Molecule 2 - COFILIN-1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	CFL1, CFL
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	18 KDA PHOSPHOPROTEIN,P18,COFILIN,NON-MUSCLE ISOFORM

Molecule 3 - COFILIN-1
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	CFL1, CFL
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	18 KDA PHOSPHOPROTEIN,P18,COFILIN,NON-MUSCLE ISOFORM

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

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

Biological Unit 1 (3, 3)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:345 , CYS A:349 , GLY A:351 , VAL A:366 , LYS A:368 , LEU A:397 , THR A:413 , GLU A:414 , ILE A:416 , THR A:420 , ASN A:465 , LEU A:467 , ASP A:478 , MG A:1002 , SEP B:3	binding site for residue ANP A 1001
2	AC2	SOFTWARE	HIS A:464 , ASN A:465 , ANP A:1001	binding site for residue MG A 1002
3	AC3	SOFTWARE	LEU C:345 , GLY C:351 , VAL C:366 , LYS C:368 , LEU C:397 , THR C:413 , GLU C:414 , ILE C:416 , THR C:420 , LEU C:467 , ASP C:478 , MG C:702 , ALA D:2 , SER D:3	binding site for residue ANP C 701
4	AC4	SOFTWARE	HIS C:464 , ASN C:465 , ANP C:701	binding site for residue MG C 702

(no "SS Bond" information available for 5HVK)

Asymmetric Unit

No.	Residues
1	Gly A:324	-	Ala A:325
2	Asp A:502	-	Arg A:503
3	Ser B:41	-	Glu B:42
4	Gly C:346	-	Lys C:347
5	Ala C:477	-	Asp C:478
6	Asp C:502	-	Arg C:503
7	Val D:60	-	Gly D:61
8	Val D:64	-	Asp D:65
9	Gly D:154	-	Gly D:155

(no "SAP(SNP)/Variant" information available for 5HVK)

(no "PROSITE Motif" information available for 5HVK)

(no "Exon" information available for 5HVK)

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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee....eeeeee......eeeeeeee.....eeeeeee......hhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee...................hhhhhh.....hhhhhhhhhhhhhhhhhh................hhhhhhhhh.......hhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvk A 324 GAMGSRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVDPDRKKRYtVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRGFWETYRR 634
                                   333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483   ||  506 |     516       526       536       546       556       566       576       586       596       606       616       626        
                                                                                                                                                                                             487|      |                                                                                                                              
                                                                                                                                                                                              501      |                                                                                                                              
                                                                                                                                                                                                     508-TPO

Chain B from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhhhhhh....hhhhhhhhheeeeeeee.....eeeeeeeeeee.........hhhhhhhhhh.....eeeeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhh.hhhhhhhhh.....ee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvk B   2 AsGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYTTFVKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKLTGIKHELQANCYEEVKDRCTLAEKLGGSAVISLEGKPL 166
                             |      11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
                             3-SEP

Chain C from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....eeeeee......eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee..................hhhhhh.....hhhhhhhhhhhhhhhhhh................hhhhhhhhh.......hhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvk C 328 SRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVPDRKKRYtVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRGFWETYR 633
                                   337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       501      |511       521       531       541       551       561       571       581       591       601       611       621       631  
                                                                                                                                                                                        486|      |                                                                                                                             
                                                                                                                                                                                         501      |                                                                                                                             
                                                                                                                                                                                                508-TPO

Chain D from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhhhhhh.....hhhhhhh.eeeeeeee.....eeeeeeeeeee.hhh.....hhhhhhhhhh.....eeeeeeeeeee..eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.......eeee.hhhhhh.hhhhhhhhh.....ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvk D   2 ASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYTTFVKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKLTGIKHELQANCYEEVKDRCTLAEKLGGSAVISLEGKP 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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 '\|'

(no "SCOP Domain" information available for 5HVK)

(no "CATH Domain" information available for 5HVK)

(no "Pfam Domain" information available for 5HVK)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ANP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SEP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TPO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala C:477 - Asp C:478	[ RasMol ]
		Asp A:502 - Arg A:503	[ RasMol ]
		Asp C:502 - Arg C:503	[ RasMol ]
		Gly A:324 - Ala A:325	[ RasMol ]
		Gly C:346 - Lys C:347	[ RasMol ]
		Gly D:154 - Gly D:155	[ RasMol ]
		Ser B:41 - Glu B:42	[ RasMol ]
		Val D:60 - Gly D:61	[ RasMol ]
		Val D:64 - Asp D:65	[ RasMol ]

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

Jmol
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	5hvk
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
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	COF1_HUMAN \| P23528
		Comparative Protein Structure Models	:	ModBase
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	LIMK1_HUMAN \| P53667
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	2.7.11.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	COF1_HUMAN \| P23528
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	LIMK1_HUMAN \| P53667
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	COF1_HUMAN \| P23528	:	1q8g 1q8x 3j0s 4bex 5l6w
	LIMK1_HUMAN \| P53667	:	3s95 5hvj 5l6w 5nxc

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (51, 58)

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Related Entries

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Related Entries Specified in the PDB File