1OGC - JenaLib

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Title :   THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH D-RIBOSE

Authors :   M. -S. Kim, B. -H. Oh

Date :   30 Apr 03 (Deposition) - 01 Sep 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   M. -S. Kim, J. Shin, W. Lee, H. -S. Lee, B. -H. Oh
Crystal Structures Of Rbsd Leading To The Identification Of Cytoplasmic Sugar-Binding Proteins With A Novel Folding Architecture
J. Biol. Chem. V. 278 28173 2003
PubMed-ID: 12738765 | Reference-DOI: 10.1074/JBC.M304523200

Molecule 1 - HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
	Chains	:	A, B, C, D, E
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	CYTOPLASMIC RIBOSE-BINDING PROTEIN RBSD

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:2 , LYS C:2	BINDING SITE FOR RESIDUE CL A1132
2	AC2	SOFTWARE	LYS D:2 , LYS E:2	BINDING SITE FOR RESIDUE CL D1133

(no "SS Bond" information available for 1OGC)

Asymmetric Unit

No.	Residues
1	Leu A:48	-	Pro A:49
2	Leu B:48	-	Pro B:49
3	Leu C:48	-	Pro C:49
4	Leu D:48	-	Pro D:49
5	Leu E:48	-	Pro E:49

(no "SAP(SNP)/Variant" information available for 1OGC)

(no "PROSITE Motif" information available for 1OGC)

(no "Exon" information available for 1OGC)

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:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogca_ A: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eeeee...........eee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh..eee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogc A   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogcb_ B: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eeeee..........eeee........hhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogc B   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogcc_ C: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eeeee..........eeee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogc C   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogcd_ D: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eeeee..........eeee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogc D   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain E from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogce_ E: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RbsD_FucU-1ogcE01 E:1-131                                                                                                           Pfam domains (1)
           Pfam domains (2) RbsD_FucU-1ogcE02 E:1-131                                                                                                           Pfam domains (2)
           Pfam domains (3) RbsD_FucU-1ogcE03 E:1-131                                                                                                           Pfam domains (3)
           Pfam domains (4) RbsD_FucU-1ogcE04 E:1-131                                                                                                           Pfam domains (4)
           Pfam domains (5) RbsD_FucU-1ogcE05 E:1-131                                                                                                           Pfam domains (5)
         Sec.struct. author .......hhhhhhhhhhh....eeeee..........eeee........hhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogc E   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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: RbsD-like (12)

Superfamily: RbsD-like (12)

Family: RbsD-like (5)

Protein domain: Ribose transport protein RbsD (4)

Bacillus subtilis [TaxId: 1423] (4)

1a	d1ogca_	A:
1b	d1ogcb_	B:
1c	d1ogcc_	C:
1d	d1ogcd_	D:
1e	d1ogce_	E:

(no "CATH Domain" information available for 1OGC)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RbsD_FucU] (9)

Family: RbsD_FucU (9)

Bacillus subtilis (4)

1a	RbsD_FucU-1ogcE01	E:1-131
1b	RbsD_FucU-1ogcE02	E:1-131
1c	RbsD_FucU-1ogcE03	E:1-131
1d	RbsD_FucU-1ogcE04	E:1-131
1e	RbsD_FucU-1ogcE05	E:1-131

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RBSD_BACSU | P36946)

molecular function
	GO:0016872	intramolecular lyase activity	The catalysis of certain rearrangements of a molecule to break or form a ring.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0048029	monosaccharide binding	Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
biological process
	GO:0019303	D-ribose catabolic process	The chemical reactions and pathways resulting in the breakdown of D-ribose (ribo-pentose).
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0005996	monosaccharide metabolic process	The chemical reactions and pathways involving monosaccharides, 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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Leu A:48 - Pro A:49	[ RasMol ]
		Leu B:48 - Pro B:49	[ RasMol ]
		Leu C:48 - Pro C:49	[ RasMol ]
		Leu D:48 - Pro D:49	[ RasMol ]
		Leu E:48 - Pro E:49	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	RBSD_BACSU \| P36946	:	1ogd 1oge 1ogf

1ogd	THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH D-RIBOSE
1oge	THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH RIBOSE 5-PHOSPHATE
1ogf	THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH GLYCEROL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (1, 5)

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Pfam Domains (1, 5)

Gene Ontology (7, 7)

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