4BEG - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF RV2140C, A PHOSPHATIDYL-ETHANOLAMINE BINDING PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SULPHATE

Authors :   S. J. Holton, M. Williams

Date :   09 Mar 13 (Deposition) - 14 Aug 13 (Release) - 25 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.42

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

Keywords :   Lipid-Binding Protein, Pebp, Rkip (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Eulenburg, V. A. Higman, A. Diehl, M. Wilmanns, S. J. Holton
Structural And Biochemical Characterization Of Rv2140C, A Phosphatidylethanolamine-Binding Protein From Mycobacterium Tuberculosis.
Febs Lett. V. 587 2936 2013
PubMed-ID: 23907008 | Reference-DOI: 10.1016/J.FEBSLET.2013.07.038

Molecule 1 - PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PETM-11
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	UPF0098 PROTEIN RV2140C/MT2198

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	GOL	12	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2178 , MET B:39 , ASP B:68 , PHE B:77 , HIS B:79 , ALA B:121 , ALA B:122 , PRO B:123 , HIS B:130 , TYR B:132	BINDING SITE FOR RESIDUE SO4 A1000
2	AC2	SOFTWARE	ASP A:68 , PHE A:77 , HIS A:79 , ALA A:122 , PRO A:123 , HIS A:130 , TYR A:132 , HOH B:2164	BINDING SITE FOR RESIDUE SO4 B1000
3	AC3	SOFTWARE	THR A:20 , SER A:21 , HOH A:2045 , GLY B:54 , PHE B:55 , HOH B:2065	BINDING SITE FOR RESIDUE GOL B1177
4	AC4	SOFTWARE	HOH A:2080 , ARG B:51 , TRP B:52 , SER B:53 , THR B:90 , HOH B:2026 , HOH B:2030 , HOH B:2165	BINDING SITE FOR RESIDUE GOL B1178
5	AC5	SOFTWARE	ALA A:10 , LEU A:11 , PRO A:12 , LYS A:13 , HOH A:2031 , HOH A:2032 , HOH A:2179 , HIS B:127	BINDING SITE FOR RESIDUE GOL A1177
6	AC6	SOFTWARE	PRO A:12 , LEU A:14 , HIS A:137 , LEU A:159 , PHE A:160 , ALA A:163 , ARG A:166 , HOH A:2148 , HOH A:2165 , HOH A:2180	BINDING SITE FOR RESIDUE GOL A1178
7	AC7	SOFTWARE	GLN A:49 , GLU A:91 , PRO A:93 , GLU A:94 , HOH A:2049 , ARG B:51 , HOH B:2092	BINDING SITE FOR RESIDUE GOL A1179
8	AC8	SOFTWARE	TYR A:67 , LEU A:74 , SER A:75 , GLY A:76 , HOH A:2093 , TYR B:67 , PRO B:69 , HOH B:2166	BINDING SITE FOR RESIDUE GOL B1179

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

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

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

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

(no "Exon" information available for 4BEG)

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:178
 aligned with Y2140_MYCTO | P9WFN0 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:178
                              1                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168        
          Y2140_MYCTO     - --MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
               SCOP domains d4bega_ A: automated matches                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eee..........hhhh...............eeee.......eeeeeeee........eeeeeeeeee....ee..............ee....................eeeeeeeeeee...........hhhhhhhhhhhheeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4beg A  -1 GAMTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168

Chain A from PDB  Type:PROTEIN  Length:178
 aligned with Y2140_MYCTU | P9WFN1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:178
                              1                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168        
          Y2140_MYCTU     - --MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
               SCOP domains d4bega_ A: automated matches                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eee..........hhhh...............eeee.......eeeeeeee........eeeeeeeeee....ee..............ee....................eeeeeeeeeee...........hhhhhhhhhhhheeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4beg A  -1 GAMTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with Y2140_MYCTO | P9WFN0 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
          Y2140_MYCTO     2 TTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
               SCOP domains d4begb_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.......ee.hhhh...............eeee.......eeeeeeee........eeeeeeeeee....ee..............ee.....................eeeeeeeeee...........hhhhhhhhhhhheeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4beg B   2 TTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with Y2140_MYCTU | P9WFN1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
          Y2140_MYCTU     2 TTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
               SCOP domains d4begb_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.......ee.hhhh...............eeee.......eeeeeeee........eeeeeeeeee....ee..............ee.....................eeeeeeeeee...........hhhhhhhhhhhheeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4beg B   2 TTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

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: PEBP-like (18)

Superfamily: PEBP-like (18)

Family: automated matches (3)

Protein domain: automated matches (3)

Mycobacterium tuberculosis [TaxId: 83332] (1)

1a	d4bega_	A:
1b	d4begb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y2140_MYCTO | P9WFN0)

Chain A,B (Y2140_MYCTU | P9WFN1)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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
		GOL	[ 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 ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	4beg
		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
	Y2140_MYCTO \| P9WFN0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Y2140_MYCTU \| P9WFN1
		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
	Y2140_MYCTO \| P9WFN0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Y2140_MYCTU \| P9WFN1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 4BEG)

4bef	STRUCTURE OF RV2140C, A PHOSPHATIDYL-ETHANOLAMINE BINDING PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

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 (3, 3)

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