3B3D - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   B.SUBTILIS YTBE

Authors :   Y. F. Zhou, L. F. Li, Y. H. Liang, X. -D. Su

Date :   20 Oct 07 (Deposition) - 21 Oct 08 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Aldo-Keto Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lei, Y. F. Zhou, L. F. Li, X. -D. Su
Structural And Biochemical Analyses Of Yvgn And Ytbe From Bacillus Subtilis
Protein Sci. V. 18 1792 2009
PubMed-ID: 19585557 | Reference-DOI: 10.1002/PRO.178

Molecule 1 - PUTATIVE MORPHINE DEHYDROGENASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YTBE
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	YTBE PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:194 , PRO A:195 , LEU A:196 , PRO A:235 , LYS A:236 , HOH A:361	BINDING SITE FOR RESIDUE CA A 281
2	AC2	SOFTWARE	PRO B:195 , LEU B:196 , LYS B:236 , HOH B:314	BINDING SITE FOR RESIDUE CA B 281
3	AC3	SOFTWARE	SER C:194 , PRO C:195 , LEU C:196 , LYS C:236 , HOH C:399	BINDING SITE FOR RESIDUE CA C 281

(no "SS Bond" information available for 3B3D)

(no "Cis Peptide Bond" information available for 3B3D)

(no "SAP(SNP)/Variant" information available for 3B3D)

Asymmetric Unit (3, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	YTBE_BACSU	44-61	3	A:44-61 B:44-61 C:44-61
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	YTBE_BACSU	130-147	3	A:130-147 B:130-147 C:130-147
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	YTBE_BACSU	234-249	3	A:234-249 B:234-249 C:234-249

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	YTBE_BACSU	44-61	1	A:44-61 - -
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	YTBE_BACSU	130-147	1	A:130-147 - -
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	YTBE_BACSU	234-249	1	A:234-249 - -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	YTBE_BACSU	44-61	1	- B:44-61 -
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	YTBE_BACSU	130-147	1	- B:130-147 -
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	YTBE_BACSU	234-249	1	- B:234-249 -

Biological Unit 3 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	YTBE_BACSU	44-61	1	- - C:44-61
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	YTBE_BACSU	130-147	1	- - C:130-147
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	YTBE_BACSU	234-249	1	- - C:234-249

(no "Exon" information available for 3B3D)

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:280
 aligned with YTBE_BACSU | O34678 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    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
           YTBE_BACSU     1 MTTHLQAKATLHNGVEMPWFGLGVFQVEEGSELVNAVKTAIVHGYRSIDTAAIYGNEAGVGEGIREGIEEAGISREDLFITSKVWNADLGYEETLAAFETSLSKLGLDYLDLYLIHWPVEGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQVEFHPRLTQKELIRYCQNQGIQMEAWSPLMQGQLLDHPVLADIAQTYNKSVAQIILRWDLQHGIITIPKSTKEHRIKENASVFDFELTQDDMNRIDALNENLRVGPDPDNFDF 280
               SCOP domains d3b3da_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3b3dA00 A:1-280 NADP-dependent oxidoreductase                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eee...ee......hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhh........eeeee......hhhhhhhhhhhh.eeeee..hhhhh...hhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b3d A   1 MTTHLQAKATLHNGVEMPWFGLGVFQVEEGSELVNAVKTAIVHGYRSIDTAAIYGNEAGVGEGIREGIEEAGISREDLFITSKVWNADLGYEETLAAFETSLSKLGLDYLDLYLIHWPVEGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQVEFHPRLTQKELIRYCQNQGIQMEAWSPLMQGQLLDHPVLADIAQTYNKSVAQIILRWDLQHGIITIPKSTKEHRIKENASVFDFELTQDDMNRIDALNENLRVGPDPDNFDF 280
                                    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

Chain B from PDB  Type:PROTEIN  Length:277
 aligned with YTBE_BACSU | O34678 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:277
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       
           YTBE_BACSU     4 HLQAKATLHNGVEMPWFGLGVFQVEEGSELVNAVKTAIVHGYRSIDTAAIYGNEAGVGEGIREGIEEAGISREDLFITSKVWNADLGYEETLAAFETSLSKLGLDYLDLYLIHWPVEGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQVEFHPRLTQKELIRYCQNQGIQMEAWSPLMQGQLLDHPVLADIAQTYNKSVAQIILRWDLQHGIITIPKSTKEHRIKENASVFDFELTQDDMNRIDALNENLRVGPDPDNFDF 280
               SCOP domains d3b3db_ B: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3b3dB00 B:4-280 NADP-dependent oxidoreductase                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....eee...ee......hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee..hhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhh.......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b3d B   4 HLQAKATLHNGVEMPWFGLGVFQVEEGSELVNAVKTAIVHGYRSIDTAAIYGNEAGVGEGIREGIEEAGISREDLFITSKVWNADLGYEETLAAFETSLSKLGLDYLDLYLIHWPVEGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQVEFHPRLTQKELIRYCQNQGIQMEAWSPLMQGQLLDHPVLADIAQTYNKSVAQIILRWDLQHGIITIPKSTKEHRIKENASVFDFELTQDDMNRIDALNENLRVGPDPDNFDF 280
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273

Chain C from PDB  Type:PROTEIN  Length:280
 aligned with YTBE_BACSU | O34678 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    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
           YTBE_BACSU     1 MTTHLQAKATLHNGVEMPWFGLGVFQVEEGSELVNAVKTAIVHGYRSIDTAAIYGNEAGVGEGIREGIEEAGISREDLFITSKVWNADLGYEETLAAFETSLSKLGLDYLDLYLIHWPVEGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQVEFHPRLTQKELIRYCQNQGIQMEAWSPLMQGQLLDHPVLADIAQTYNKSVAQIILRWDLQHGIITIPKSTKEHRIKENASVFDFELTQDDMNRIDALNENLRVGPDPDNFDF 280
               SCOP domains d3b3dc_ C: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3b3dC00 C:1-280 NADP-dependent oxidoreductase                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eee...ee......hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhh........eeeee......hhhhhhhhhhhh.eeeee..hhhhh...hhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhh.......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b3d C   1 MTTHLQAKATLHNGVEMPWFGLGVFQVEEGSELVNAVKTAIVHGYRSIDTAAIYGNEAGVGEGIREGIEEAGISREDLFITSKVWNADLGYEETLAAFETSLSKLGLDYLDLYLIHWPVEGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQVEFHPRLTQKELIRYCQNQGIQMEAWSPLMQGQLLDHPVLADIAQTYNKSVAQIILRWDLQHGIITIPKSTKEHRIKENASVFDFELTQDDMNRIDALNENLRVGPDPDNFDF 280
                                    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

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: TIM beta/alpha-barrel (3956)

Superfamily: NAD(P)-linked oxidoreductase (286)

Family: automated matches (35)

Protein domain: automated matches (35)

Bacillus subtilis [TaxId: 1423] (3)

1a	d3b3da_	A:
1b	d3b3db_	B:
1c	d3b3dc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: NADP-dependent oxidoreductase (181)

Bacillus subtilis. Organism_taxid: 1423. (5)

1a	3b3dA00	A:1-280
1b	3b3dC00	C:1-280
1c	3b3dB00	B:4-280

(no "Pfam Domain" information available for 3B3D)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (YTBE_BACSU | O34678)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric Unit
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Biological Units
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Description

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