3C6Q - 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 :   APO AND LIGAND-BOUND FORM OF A THERMOPHILIC GLUCOSE/XYLOSE BINDING PROTEIN

Authors :   M. J. Cuneo, H. W. Hellinga

Date :   05 Feb 08 (Deposition) - 26 Feb 08 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Glucose Binding Protein, Xylose Binding Protein, Periplasmic Binding Protein, Glucose, Xylose, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Cuneo, H. W. Hellinga
Open To Closed Transition Of A Thermophilic Glucose Binding Protein
To Be Published
PubMed: search

Molecule 1 - SUGAR ABC TRANSPORTER, PERIPLASMIC SUGAR-BINDING PROTEIN
	Chains	:	B, A, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 32-335
	Gene	:	TM0114
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	XYP	-1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	XYP	-1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS C:9 , TYR C:14 , TRP C:15 , ASP C:89 , ASN C:137 , ARG C:141 , GLU C:164 , TYR C:190 , ALA C:191 , ASP C:216 , GLN C:236	BINDING SITE FOR RESIDUE XYP C 500
2	AC2	SOFTWARE	LYS D:9 , TRP D:15 , ASP D:89 , ASN D:137 , ARG D:141 , GLU D:164 , TYR D:190 , ALA D:191 , ASP D:216 , GLN D:236	BINDING SITE FOR RESIDUE XYP D 501

(no "SS Bond" information available for 3C6Q)

(no "Cis Peptide Bond" information available for 3C6Q)

(no "SAP(SNP)/Variant" information available for 3C6Q)

(no "PROSITE Motif" information available for 3C6Q)

(no "Exon" information available for 3C6Q)

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:305
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:305
                                    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     
         Q9WXW9_THEMA    31 ALTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 335
               SCOP domains d3c6qa_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3c6qA01 A:1-103,A:236-280  [code=3.40.50.2300, no name defined]                                        3c6qA02 A:104-235,A:281-305  [code=3.40.50.2300, no name defined]                                                                   3c6qA01 A:1-103,A:236-280                    3c6qA02                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhh...eeee..........eeee.hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeeee..eeee...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6q A   1 MLTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKCDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDCEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 305
                                    10        20        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

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:305
                                    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     
         Q9WXW9_THEMA    31 ALTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 335
               SCOP domains d3c6qb_ B: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3c6qB01 B:1-103,B:236-280  [code=3.40.50.2300, no name defined]                                        3c6qB02 B:104-235,B:281-305  [code=3.40.50.2300, no name defined]                                                                   3c6qB01 B:1-103,B:236-280                    3c6qB02                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhh...eeee..........eeee.hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeeee..eeee...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6q B   1 MLTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKCDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDCEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 305
                                    10        20        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

Chain C from PDB  Type:PROTEIN  Length:305
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:305
                                    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     
         Q9WXW9_THEMA    31 ALTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 335
               SCOP domains d3c6qc_ C: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3c6qC01 C:1-103,C:236-280  [code=3.40.50.2300, no name defined]                                        3c6qC02 C:104-235,C:281-305  [code=3.40.50.2300, no name defined]                                                                   3c6qC01 C:1-103,C:236-280                    3c6qC02                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeee...hhhhh...eee.hhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee......eeeee...eee...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6q C   1 MLTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKCDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDCEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 305
                                    10        20        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

Chain D from PDB  Type:PROTEIN  Length:305
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:305
                                    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     
         Q9WXW9_THEMA    31 ALTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 335
               SCOP domains d3c6qd_ D: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3c6qD01 D:1-103,D:236-280  [code=3.40.50.2300, no name defined]                                        3c6qD02 D:104-235,D:281-305  [code=3.40.50.2300, no name defined]                                                                   3c6qD01 D:1-103,D:236-280                    3c6qD02                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeee...hhhhh...eee.hhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee......eeeee...eee...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6q D   1 MLTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKCDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDCEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPIKF 305
                                    10        20        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

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 I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: automated matches (65)

Protein domain: automated matches (65)

Thermotoga maritima [TaxId: 243274] (4)

1a	d3c6qa_	A:
1b	d3c6qb_	B:
1c	d3c6qc_	C:
1d	d3c6qd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Thermotoga maritima. Organism_taxid: 2336. (8)

1a	3c6qA01	A:1-103,A:236-280
1b	3c6qB01	B:1-103,B:236-280
1c	3c6qC01	C:1-103,C:236-280
1d	3c6qD01	D:1-103,D:236-280
1e	3c6qA02	A:104-235,A:281-305
1f	3c6qB02	B:104-235,B:281-305
1g	3c6qC02	C:104-235,C:281-305
1h	3c6qD02	D:104-235,D:281-305

(no "Pfam Domain" information available for 3C6Q)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9WXW9_THEMA | Q9WXW9)

molecular function
	GO:0015145	monosaccharide transmembrane transporter activity	Enables the transfer of a monosaccharide from one side of a membrane to the other.
biological process
	GO:0015749	monosaccharide transport	The directed movement of monosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	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.

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	Q9WXW9_THEMA \| Q9WXW9	:	2h3h 2qvc

2h3h	CRYSTAL STRUCTURE OF THE LIGANDED FORM OF THERMOTOGA MARITIMA GLUCOSE BINDING PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

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Related Entries Specified in the PDB File