4PFW - 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)

Title :   CRYSTAL STRUCTURE OF MANNOHEXAOSE BOUND OLIGOPEPTIDE ABC TRANSPORTER, PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN (TM1226) FROM THERMOTOGA MARITIMA AT 2.2 A RESOLUTION

Authors :   X. Lu, S. Ghimire-Rijal, M. J. Cuneo

Date :   30 Apr 14 (Deposition) - 17 Sep 14 (Release) - 05 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ghimire-Rijal, X. Lu, D. A. Myles, M. J. Cuneo
Duplication Of Genes In An Atp-Binding Cassette Transport System Increases Dynamic Range While Maintaining Ligand Specificity.
J. Biol. Chem. V. 289 30090 2014
PubMed-ID: 25210043 | Reference-DOI: 10.1074/JBC.M114.590992

Molecule 1 - ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	THEMA_08200, TMARI_1233
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
	Synonym	:	MANNOSIDE ABC TRANSPORT SYSTEM,SUGAR-BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 22)

No.	Name	Count	Type	Full Name
1	BMA	8	Ligand/Ion	BETA-D-MANNOSE
2	GOL	3	Ligand/Ion	GLYCEROL
3	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	BMA	4	Ligand/Ion	BETA-D-MANNOSE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 10)

No.	Name	Count	Type	Full Name
1	BMA	4	Ligand/Ion	BETA-D-MANNOSE
2	GOL	3	Ligand/Ion	GLYCEROL
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:362 , ASN A:364 , ASP A:366 , PHE A:368 , GLU A:370	binding site for residue MG A 601
02	AC2	SOFTWARE	GLY A:79 , GLU A:80 , TRP A:81 , HOH A:922 , HOH B:878	binding site for residue SO4 A 608
03	AC3	SOFTWARE	ARG A:109 , ILE A:133 , GLU A:134 , THR A:135	binding site for residue SO4 A 609
04	AC4	SOFTWARE	SER A:457 , GLU A:458 , PHE A:459	binding site for residue SO4 A 610
05	AC5	SOFTWARE	TRP A:81 , TYR A:150	binding site for residue SO4 A 611
06	AC6	SOFTWARE	ASP B:362 , ASN B:364 , ASP B:366 , PHE B:368 , GLU B:370	binding site for residue MG B 601
07	AC7	SOFTWARE	GLU B:155 , TYR B:158 , ILE B:438 , SER B:439 , ASN B:543 , TRP B:544 , BMA B:604 , HOH B:788 , HOH B:812	binding site for residue GOL B 608
08	AC8	SOFTWARE	TRP B:443 , ASN B:447 , TYR B:451 , PRO B:452 , GLU B:478 , ASN B:481 , HOH B:932	binding site for residue GOL B 609
09	AC9	SOFTWARE	TRP B:47 , TYR B:419 , TYR B:423 , ASN B:434 , BMA B:604 , BMA B:605 , HOH B:967	binding site for residue GOL B 610
10	AD1	SOFTWARE	ARG B:109 , ILE B:133 , GLU B:134 , THR B:135 , HOH B:899	binding site for residue SO4 B 611
11	AD2	SOFTWARE	GLY A:32 , SER A:33 , TRP A:35 , HIS A:122 , SER A:125 , GLU A:152 , ASN A:231 , ASN A:247 , PHE A:248 , MET A:249 , TRP A:387 , ASP A:389 , TRP A:390 , ALA A:433 , ASN A:434 , GLY A:435 , THR A:436 , GLY A:437 , TYR A:451 , TYR A:461 , THR A:462 , TRP A:541 , ALA A:542 , ASN A:543 , TRP A:544 , HOH A:724 , HOH A:730 , HOH A:737 , HOH A:738 , HOH A:745 , HOH A:750 , HOH A:789 , HOH A:830	binding site for Poly-Saccharide residues MAN A 602 through BMA A 607
12	AD3	SOFTWARE	GLY A:32 , SER A:33 , TRP A:35 , HIS A:122 , SER A:125 , GLU A:152 , ASN A:231 , ASN A:247 , PHE A:248 , MET A:249 , TRP A:387 , ASP A:389 , TRP A:390 , ALA A:433 , ASN A:434 , GLY A:435 , THR A:436 , GLY A:437 , TYR A:451 , TYR A:461 , THR A:462 , TRP A:541 , ALA A:542 , ASN A:543 , TRP A:544 , HOH A:724 , HOH A:730 , HOH A:737 , HOH A:738 , HOH A:745 , HOH A:750 , HOH A:789 , HOH A:830 , GLY B:32 , SER B:33 , TRP B:35 , HIS B:122 , TYR B:123 , SER B:125 , GLU B:152 , ASN B:231 , ASN B:247 , PHE B:248 , MET B:249 , TRP B:387 , ASP B:389 , TRP B:390 , ALA B:433 , ASN B:434 , GLY B:435 , THR B:436 , GLY B:437 , TYR B:451 , TYR B:461 , THR B:462 , TRP B:541 , ALA B:542 , ASN B:543 , TRP B:544 , GOL B:608 , GOL B:610 , HOH B:749 , HOH B:768 , HOH B:776 , HOH B:803 , HOH B:832 , HOH B:837 , HOH B:914 , HOH B:934	binding site for Poly-Saccharide residues MAN B 602 through BMA B 607

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

Asymmetric Unit

No.	Residues
1	Pro A:269	-	Pro A:270
2	Tyr A:287	-	Pro A:288
3	Pro B:269	-	Pro B:270
4	Tyr B:287	-	Pro B:288

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

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

(no "Exon" information available for 4PFW)

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:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhh.eeeee....................hhhhhh....eee......eee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhh....hhhhhh.eeeeeeee..eeeeee...hhhhhhhhhhhh...hhhhhh..hhhhhhhh..........eeeeeee..eeeeee...hhhhhhhh......eeeee...hhhhhhhhhhh....ee.....hhhhhhhhhh...........eeeeeeeeee........hhhhhhhhhhhh.hhhhhhh......ee.........hhhhhhhhhhhhhhhh...hhhhhhhhhhhh...................eeeee....hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee..ee....ee.................hhhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pfw A  21 VLERNETMYYGGSLWSPPSNWNPFTPWNAVPGTTGLVYETMFFYDPLTGNFDPWLAEKGEWLDSKTYRVVLREGIYWHDNVPLTSEDVRFTFEIAKKYKGIHYSSVWEWLDHIETPDNRTVIFVFKDPRYHEWNELLYTLPIVPKHIWEEKDETTILQSSNEYPLGSGPYVAHSWDQNKMIFERFENWWGTKVMGVKPAPKYVVIVRVLSNNVALGMLMKGELDFSNFMLPGVPILKKVYNLNTWYDEPPYHLSSTVVGLFLNARKYPLSLPEFRRAIAMSINADPIVQRVYEGAVLKADPLGFLPNSVWMKYYPKEVVEKHGFKYDPEEAKSILDKLGFRDVNGDGFRETPDGKPIKLTIECPYGWTDWMQAIQVIVDQLKVVGINAEPYFPDSSKYYENMYKGEFDIEMNANGTGISSTPWTYFNTIFYPDALESEFSYTGNYGRYQNPEVESLLEELNRTPLDNVEKVTELCGKLGEILLKDLPFIPLWYGAMAFITQDNVWTNWPNEHNPYAWPCGWANWWQTGALKILFNLKPAK 560
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560

Chain B from PDB  Type:PROTEIN  Length:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhh.eeeee....................hhhhhh....eee......eee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhh....hhhhhh.eeeee.....eeeeee...hhhhhhhhhhhh...hhhhhh..hhhhhhhh..........eeeeeee..eeeeee...hhhhhhhh......eeeee...hhhhhhhhhhh....ee.....hhhhhhhh.............eeeeeeeeee........hhhhhhhhhhhh.hhhhhhhh.....ee.........hhhhhhhhhhhhhhhh...hhhhhhhhhhhh...................eeeee....hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee..ee....ee.................hhhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pfw B  21 VLERNETMYYGGSLWSPPSNWNPFTPWNAVPGTTGLVYETMFFYDPLTGNFDPWLAEKGEWLDSKTYRVVLREGIYWHDNVPLTSEDVRFTFEIAKKYKGIHYSSVWEWLDHIETPDNRTVIFVFKDPRYHEWNELLYTLPIVPKHIWEEKDETTILQSSNEYPLGSGPYVAHSWDQNKMIFERFENWWGTKVMGVKPAPKYVVIVRVLSNNVALGMLMKGELDFSNFMLPGVPILKKVYNLNTWYDEPPYHLSSTVVGLFLNARKYPLSLPEFRRAIAMSINADPIVQRVYEGAVLKADPLGFLPNSVWMKYYPKEVVEKHGFKYDPEEAKSILDKLGFRDVNGDGFRETPDGKPIKLTIECPYGWTDWMQAIQVIVDQLKVVGINAEPYFPDSSKYYENMYKGEFDIEMNANGTGISSTPWTYFNTIFYPDALESEFSYTGNYGRYQNPEVESLLEELNRTPLDNVEKVTELCGKLGEILLKDLPFIPLWYGAMAFITQDNVWTNWPNEHNPYAWPCGWANWWQTGALKILFNLKPAK 560
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560

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 4PFW)

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

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

Asymmetric Unit(hide GO term definitions)

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
		BMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ 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 ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		AD1	[ RasMol ]	+environment [ RasMol ]
		AD2	[ RasMol ]	+environment [ RasMol ]
		AD3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Pro A:269 - Pro A:270	[ RasMol ]
		Pro B:269 - Pro B:270	[ RasMol ]
		Tyr A:287 - Pro A:288	[ RasMol ]
		Tyr B:287 - Pro B:288	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 ](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
	4pfw
		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
	G4FEC0_THEMA \| G4FEC0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	G4FEC0_THEMA \| G4FEC0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	G4FEC0_THEMA \| G4FEC0	:	5hm4
UniProtKB/TrEMBL
	G4FEC0_THEMA \| G4FEC0	:	4pfu

4pft
4pfu	SAME PROTEIN, DIFFERENT LIGAND
4pfy

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 22)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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 (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