4A1Y - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   HUMAN MYELIN P2 PROTEIN, K65Q MUTANT

Authors :   M. Lehtimaki, P. Kursula

Date :   20 Sep 11 (Deposition) - 10 Oct 12 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Lehtimaki, P. Kursula
Structure-Function Relationships In The Myelin Peripheral Membrane Protein P2
To Be Published
PubMed: search

Molecule 1 - MYELIN P2 PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTH27
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PERIPHERAL MYELIN PROTEIN 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	PLM	4	Ligand/Ion	PALMITIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PLM	1	Ligand/Ion	PALMITIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PLM	1	Ligand/Ion	PALMITIC ACID

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PLM	1	Ligand/Ion	PALMITIC ACID

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PLM	1	Ligand/Ion	PALMITIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:55 , ARG A:106 , ARG A:126 , TYR A:128 , HOH A:1157 , HOH A:1221	BINDING SITE FOR RESIDUE PLM A1132
2	AC2	SOFTWARE	LYS A:37 , SER A:55 , THR A:56	BINDING SITE FOR RESIDUE CL A1133
3	AC3	SOFTWARE	MET B:20 , THR B:29 , ASP B:76 , ARG B:106 , ARG B:126 , TYR B:128 , HOH B:1336 , HOH B:1351	BINDING SITE FOR RESIDUE PLM B1132
4	AC4	SOFTWARE	MET C:20 , GLY C:33 , ARG C:106 , ARG C:126 , TYR C:128 , HOH C:1369 , HOH C:1370	BINDING SITE FOR RESIDUE PLM C1132
5	AC5	SOFTWARE	LYS C:37 , SER C:55 , THR C:56	BINDING SITE FOR RESIDUE CL C1133
6	AC6	SOFTWARE	LYS D:37 , SER D:55 , THR D:56	BINDING SITE FOR RESIDUE CL D1132
7	AC7	SOFTWARE	ASP D:76 , ARG D:106 , ARG D:126 , TYR D:128 , HOH D:1354 , HOH D:1355	BINDING SITE FOR RESIDUE PLM D1133

(no "SS Bond" information available for 4A1Y)

(no "Cis Peptide Bond" information available for 4A1Y)

(no "SAP(SNP)/Variant" information available for 4A1Y)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	MYP2_HUMAN	7-24	4	A:6-23 B:6-23 C:6-23 D:6-23

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	MYP2_HUMAN	7-24	1	A:6-23 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	MYP2_HUMAN	7-24	1	- B:6-23 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	MYP2_HUMAN	7-24	1	- - C:6-23 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	MYP2_HUMAN	7-24	1	- - - D:6-23

(no "Exon" information available for 4A1Y)

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:133
 aligned with MYP2_HUMAN | P02689 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:133
                             1                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129   
           MYP2_HUMAN     - -MSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFKLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 132
               SCOP domains d4a1ya_ A: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeeeehhhhhhhhhh.hhhhhhhhhhh..eeeeeee..eeeeeeee..eeeeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------FABP  PDB: A:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a1y A  -1 GMSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFQLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with MYP2_HUMAN | P02689 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:133
                             1                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129   
           MYP2_HUMAN     - -MSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFKLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 132
               SCOP domains d4a1yb_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeeeehhhhhhhhhh.hhhhhhhhhhh..eeeeeee..eeeeeee....eeeeeee....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------FABP  PDB: B:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a1y B  -1 GMSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFQLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain C from PDB  Type:PROTEIN  Length:133
 aligned with MYP2_HUMAN | P02689 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:133
                             1                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129   
           MYP2_HUMAN     - -MSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFKLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 132
               SCOP domains d4a1yc_ C: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeeeehhhhhhhhhh.hhhhhhhhhhh..eeeeeee..eeeeeeee..eeeeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------FABP  PDB: C:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a1y C  -1 GMSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFQLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain D from PDB  Type:PROTEIN  Length:133
 aligned with MYP2_HUMAN | P02689 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:133
                             1                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129   
           MYP2_HUMAN     - -MSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFKLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 132
               SCOP domains d4a1yd_ D: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeeeehhhhhhhhhh.hhhhhhhhhhh..eeeeeee..eeeeeee....eeeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------FABP  PDB: D:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a1y D  -1 GMSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFQLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

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: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Fatty acid binding protein-like (183)

Protein domain: automated matches (26)

Human (Homo sapiens) [TaxId: 9606] (15)

1a	d4a1ya_	A:
1b	d4a1yb_	B:
1c	d4a1yc_	C:
1d	d4a1yd_	D:

(no "CATH Domain" information available for 4A1Y)

(no "Pfam Domain" information available for 4A1Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MYP2_HUMAN | P02689)

molecular function
	GO:0015485	cholesterol binding	Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0005504	fatty acid binding	Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0061024	membrane organization	A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

Asymmetric 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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PLM	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4a1y)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	4a1y
		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
	MYP2_HUMAN \| P02689
		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
	MYP2_HUMAN \| P02689
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MYP2_HUMAN \| P02689	:	2wut 3nr3 4a1h 4a8z 4bvm 4d6a 4d6b

2wut	CRYSTAL STRUCTURE OF HUMAN MYELIN PROTEIN P2 IN COMPLEX WITH PALMITATE
4a1h	HUMAN MYELIN P2 PROTEIN, K45S MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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