3VVF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TTC0807 COMPLEXED WITH ARGININE

Authors :   T. Tomita, Y. Kanemaru, F. Hasebe, T. Kuzuyama, M. Nishiyama

Date :   21 Jul 12 (Deposition) - 26 Jun 13 (Release) - 04 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Arginine-Complex, Periplasm Substrate Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kanemaru, F. Hasebe, T. Tomita, T. Kuzuyama, M. Nishiyama
Two Atp-Binding Cassette Transporters Involved In (S)-2-Aminoethyl-Cysteine Uptake In Thermus Thermophilus
J. Bacteriol. V. 195 3845 2013
PubMed-ID: 23794618 | Reference-DOI: 10.1128/JB.00202-13

Molecule 1 - AMINO ACID ABC TRANSPORTER, BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHIS8-TTC0807
	Expression System Strain	:	BL21 CODON PLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 19-254
	Gene	:	TTC0807, TT_C0807
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	262724
	Strain	:	HB27 / ATCC BAA-163 / DSM 7039

		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 (2, 6)

No.	Name	Count	Type	Full Name
1	ARG	2	Mod. Amino Acid	ARGININE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ARG	1	Mod. Amino Acid	ARGININE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ARG	1	Mod. Amino Acid	ARGININE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:19 , PHE A:22 , ASN A:26 , PHE A:60 , ALA A:77 , SER A:78 , GLY A:80 , ARG A:85 , GLN A:123 , THR A:126 , THR A:127 , TYR A:128 , GLU A:191 , HOH A:402	BINDING SITE FOR RESIDUE ARG A 301
2	AC2	SOFTWARE	TYR A:27 , ASP A:29 , GLU A:30 , TYR B:27 , ASP B:29 , GLU B:30	BINDING SITE FOR RESIDUE SO4 A 302
3	AC3	SOFTWARE	ARG A:110 , LYS A:113 , GLU B:231 , ASP B:232 , HOH B:428 , HOH B:448	BINDING SITE FOR RESIDUE SO4 A 303
4	AC4	SOFTWARE	GLU B:19 , PHE B:22 , ASN B:26 , PHE B:60 , ALA B:77 , SER B:78 , GLY B:80 , ARG B:85 , GLN B:123 , THR B:126 , THR B:127 , TYR B:128 , GLU B:191 , HOH B:403	BINDING SITE FOR RESIDUE ARG B 301
5	AC5	SOFTWARE	LYS A:134 , ARG B:48 , GLU B:214	BINDING SITE FOR RESIDUE SO4 B 302
6	AC6	SOFTWARE	LYS A:113 , ASN B:201 , LYS B:202 , SER B:203	BINDING SITE FOR RESIDUE SO4 B 303

Asymmetric Unit

No.	Residues
1	A:97	-	A:235
2	B:97	-	B:235

Asymmetric Unit

No.	Residues
1	Pro A:23	-	Pro A:24
2	Pro B:23	-	Pro B:24

(no "SAP(SNP)/Variant" information available for 3VVF)

(no "PROSITE Motif" information available for 3VVF)

(no "Exon" information available for 3VVF)

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:242
 aligned with Q72JG5_THET2 | Q72JG5 from UniProtKB/TrEMBL  Length:254

    Alignment length:242
                                                                                                                                                                                                                                                                          254 
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253| 
         Q72JG5_THET2    14 GAALAQVRSFEEIKRSGEIRIGTEGAFPPFNYFDERNQLTGFEVDLGNAIAERLGLKPRWIAQSFDTLLIQLNQGRFDFVIASHGITEERARAVDFTNPHYCTGGVIVSRKGGPRTAKDLQGKVVGVQVGTTYMEAAQKIPGIKEVRTYQRDPDALQDLLAGRIDTWITDRFVAKEAIKERKLENTLQVGELVFQERVAMAVAKGNKSLLDALNRALAELMQDGTYARISQKWFGEDVRCK-   -
               SCOP domains d3vvfa_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhheeeeee..ee...eee.....eehhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeeeee.hhhhhh.eee....eeeeeeeeee.....hhhhhh..eeeee..hhhhhhhhh.....eeeee.hhhhhhhhhhh....eeeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vvf A  -4 GGSEFQVRSFEEIKRSGEIRIGTEGAFPPFNYFDERNQLTGFEVDLGNAIAERLGLKPRWIAQSFDTLLIQLNQGRFDFVIASHGITEERARAVDFTNPHYCTGGVIVSRKGGPRTAKDLQGKVVGVQVGTTYMEAAQKIPGIKEVRTYQRDPDALQDLLAGRIDTWITDRFVAKEAIKERKLENTLQVGELVFQERVAMAVAKGNKSLLDALNRALAELMQDGTYARISQKWFGEDVRCKR 301
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235||
                                                                                                                                                                                                                                                                          236|
                                                                                                                                                                                                                                                                           301

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with Q72JG5_THET2 | Q72JG5 from UniProtKB/TrEMBL  Length:254

    Alignment length:242
                                                                                                                                                                                                                                                                          254 
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253| 
         Q72JG5_THET2    14 GAALAQVRSFEEIKRSGEIRIGTEGAFPPFNYFDERNQLTGFEVDLGNAIAERLGLKPRWIAQSFDTLLIQLNQGRFDFVIASHGITEERARAVDFTNPHYCTGGVIVSRKGGPRTAKDLQGKVVGVQVGTTYMEAAQKIPGIKEVRTYQRDPDALQDLLAGRIDTWITDRFVAKEAIKERKLENTLQVGELVFQERVAMAVAKGNKSLLDALNRALAELMQDGTYARISQKWFGEDVRCK-   -
               SCOP domains d3vvfb_ B: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhhhheeeeee..ee...eee.....eehhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...ee......hhhhhh.eeeeeeeeeeeeeeeee......hhhhh..eeeee..hhhhhhhh......eeeee.hhhhhhhhhhh....eeeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vvf B  -4 GGSEFQVRSFEEIKRSGEIRIGTEGAFPPFNYFDERNQLTGFEVDLGNAIAERLGLKPRWIAQSFDTLLIQLNQGRFDFVIASHGITEERARAVDFTNPHYCTGGVIVSRKGGPRTAKDLQGKVVGVQVGTTYMEAAQKIPGIKEVRTYQRDPDALQDLLAGRIDTWITDRFVAKEAIKERKLENTLQVGELVFQERVAMAVAKGNKSLLDALNRALAELMQDGTYARISQKWFGEDVRCKR 301
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235||
                                                                                                                                                                                                                                                                          236|
                                                                                                                                                                                                                                                                           301

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: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: automated matches (267)

Protein domain: automated matches (267)

Thermus thermophilus [TaxId: 262724] (5)

1a	d3vvfa_	A:
1b	d3vvfb_	B:

(no "CATH Domain" information available for 3VVF)

(no "Pfam Domain" information available for 3VVF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q72JG5_THET2 | Q72JG5)

molecular function
	GO:0004970	ionotropic glutamate receptor activity	Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
	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:0035235	ionotropic glutamate receptor signaling pathway	A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
		Pro A:23 - Pro A:24	[ RasMol ]
		Pro B:23 - Pro B:24	[ RasMol ]

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

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	3vvf
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	Q72JG5_THET2 \| Q72JG5	:	3vv5 3vvd 3vve

Description

Compounds

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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