2KIN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   KINESIN (MONOMERIC) FROM RATTUS NORVEGICUS

Authors :   S. Sack, J. Muller, F. Kozielski, A. Marx, M. Thormahlen, V. Biou, E. - M. Mandelkow, S. T. Brady, E. Mandelkow

Date :   28 Apr 97 (Deposition) - 08 Apr 98 (Release) - 28 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Motor Protein, Cytoskeleton (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sack, J. Muller, A. Marx, M. Thormahlen, E. M. Mandelkow, S. T. Brady, E. Mandelkow
X-Ray Structure Of Motor And Neck Domains From Rat Brain Kinesin.
Biochemistry V. 36 16155 1997
PubMed-ID: 9405049 | Reference-DOI: 10.1021/BI9722498
(for further references see the PDB file header)

Molecule 1 - KINESIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	HEAVY CHAIN, MOTOR DOMAIN
	Mutation	:	YES
	Organ	:	BRAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

Molecule 2 - KINESIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	HEAVY CHAIN, MOTOR DOMAIN
	Mutation	:	YES
	Organ	:	BRAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:98 , LYS A:99 , LEU A:100 , ARG A:162 , HOH A:550	BINDING SITE FOR RESIDUE SO4 A 502
2	AC2	SOFTWARE	ARG A:162 , ARG A:191 , HIS A:192 , MET A:198 , HOH A:606	BINDING SITE FOR RESIDUE SO4 A 504
3	AC3	SOFTWARE	LYS A:160 , ASN A:161 , VAL A:195 , THR A:196 , ASN A:197 , MET A:198 , HOH A:530 , HOH A:544 , HOH A:563	BINDING SITE FOR RESIDUE SO4 A 505
4	AC4	SOFTWARE	ARG A:14 , ARG A:16 , PRO A:17 , GLN A:87 , THR A:88 , SER A:89 , SER A:90 , GLY A:91 , LYS A:92 , THR A:93 , HIS A:94 , GLU A:125 , HOH A:522 , HOH A:556 , HOH A:570 , HOH A:643 , HOH A:644 , HOH A:651	BINDING SITE FOR RESIDUE ADP A 400

(no "SS Bond" information available for 2KIN)

(no "Cis Peptide Bond" information available for 2KIN)

(no "SAP(SNP)/Variant" information available for 2KIN)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KINESIN_MOTOR_2	PS50067	Kinesin motor domain profile.	KIF5C_RAT	8-239	1	A:8-239
2	KINESIN_MOTOR_1	PS00411	Kinesin motor domain signature.	KIF5C_RAT	226-237	1	A:226-237

(no "Exon" information available for 2KIN)

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:238
 aligned with KIF5C_RAT | P56536 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
            KIF5C_RAT     2 ADPAECSIKVMCRFRPLNEAEILRGDKFIPKFKGEETVVIGQGKPYVFDRVLPPNTTQEQVYNACAKQIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEKV 239
               SCOP domains d2kin.1 A:,B: Kinesin                                                                                                                                                                                                                          SCOP domains
               CATH domains 2kinA00 A:2-239 Kinesin                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------Kinesin-2kinA01 A:14-239                                                                                                                                                                                                           Pfam domains
         Sec.struct. author ...eeee.eeeeeee...hhhhh......eeee...eeee.........eee.....hhhhhhhh.hhhhhhhhh..eeeeeee......hhhhh...........hhhhhhhhhhhhhhh....eeeeeeeeeeeee..eeee..........eee.....eee.....eee..hhhhhhhhhhhhhhhh.....hhhhhhh.eeeeeeeeeeee.....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------KINESIN_MOTOR_2  PDB: A:8-239 UniProt: 8-239                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO-- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kin A   2 ADPAECSIKVMCRFRPLNEAEILRGDKFIPKFKGEETVVIGQGKPYVFDRVLPPNTTQEQVYNACAKQIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEKV 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with KIF5A_RAT | Q6QLM7 from UniProtKB/Swiss-Prot  Length:1027

    Alignment length:100
                                   261       271       281       291       301       311       321       331       341       351
            KIF5A_RAT   252 AKNINKSLSALGNVISALAEGTKSYVPYRDSKMTRILQDSLGGNCRTTMFICCSPSSYNDAETKSTLMFGQRAKTIKNTASVNLELTAEQWKKKYEKEKE 351
               SCOP domains d2kin.1 A:,B: Kinesin                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Kinesin-2kinB01 B:252-327                                                   ------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.......hhh.hhhhh.hhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh.eeee..eee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2kin B 252 AKNINKSLSALGNVISALAEGTKTHVPYRDSKMTRILQDSLDGNCRTTIVICCSPSVFNEAETKSTLMFGQRAKTIKNTVSVNLELTAEEWKKKYEKEKE 351
                                   261       271       281       291       301       311       321       331       341       351

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) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Motor proteins (119)

Protein domain: Kinesin (31)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

d2kin.1

A:,B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Kinesin (69)

Homologous Superfamily: Kinesin (69)

Norway rat (Rattus norvegicus) (2)

2kinA00

A:2-239

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Kinesin (42)

Rattus norvegicus (Rat) (1)

1a	Kinesin-2kinB01	B:252-327
1b	Kinesin-2kinA01	A:14-239

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (KIF5C_RAT | P56536)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008574	ATP-dependent microtubule motor activity, plus-end-directed	Catalysis of movement along a microtubule toward the plus end, coupled to the hydrolysis of ATP.
	GO:0034190	apolipoprotein receptor binding	Interacting selectively and non-covalently with an apolipoprotein receptor.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	GO:0003777	microtubule motor activity	Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0030705	cytoskeleton-dependent intracellular transport	The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007018	microtubule-based movement	A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
	GO:0008104	protein localization	Any process in which a protein is transported to, or maintained in, a specific location.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005871	kinesin complex	Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

Chain B (KIF5A_RAT | Q6QLM7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008574	ATP-dependent microtubule motor activity, plus-end-directed	Catalysis of movement along a microtubule toward the plus end, coupled to the hydrolysis of ATP.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	GO:0003777	microtubule motor activity	Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0030705	cytoskeleton-dependent intracellular transport	The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
	GO:0007018	microtubule-based movement	A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
	GO:0007017	microtubule-based process	Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
	GO:0008104	protein localization	Any process in which a protein is transported to, or maintained in, a specific location.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005871	kinesin complex	Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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
(no "Cis Peptide Bonds" information available for 2kin)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2kin
		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
	KIF5A_RAT \| Q6QLM7
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	KIF5C_RAT \| P56536
		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)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(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
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	KIF5A_RAT \| Q6QLM7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	KIF5C_RAT \| P56536
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	KIF5A_RAT \| Q6QLM7	:	3kin
	KIF5C_RAT \| P56536	:	3kin

(no "Related Entries Specified in the PDB File" available for 2KIN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 2)

Gene Ontology (21, 35)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File