1S5A - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PUTATIVE ISOMERASE FROM BACILLUS SUBTILIS

Authors :   Y. Kim, L. Lezondra, A. Joachimiak, Midwest Center For Structural (Mcsg)

Date :   20 Jan 04 (Deposition) - 11 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Structural Genomics, Hypothetical Protein, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, L. Lezondra, A. Joachimiak
The Crystal Structure Of Apc1116 From Bacillus Subtilis
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN YESE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YESE, BSU06870
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 29)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	MSE	19	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:64 , TYR A:104 , TYR A:108 , TRP A:126 , GOL A:702 , HOH A:838	BINDING SITE FOR RESIDUE ACT A 801
02	AC2	SOFTWARE	TYR C:64 , TYR C:104 , TYR C:108 , GOL C:703 , HOH C:824	BINDING SITE FOR RESIDUE ACT C 802
03	AC3	SOFTWARE	TYR B:64 , TYR B:104 , TYR B:108 , LEU B:140 , GOL B:704	BINDING SITE FOR RESIDUE ACT B 803
04	AC4	SOFTWARE	TYR D:64 , TYR D:104 , TYR D:108 , GOL D:705	BINDING SITE FOR RESIDUE ACT D 804
05	AC5	SOFTWARE	SER A:81 , SER A:84 , HOH A:802 , HOH A:814 , HOH A:885 , ARG B:14 , MSE B:17 , PRO B:76 , TYR D:79	BINDING SITE FOR RESIDUE GOL A 701
06	AC6	SOFTWARE	PHE A:38 , TYR A:108 , ASP A:124 , ACT A:801 , HOH A:810 , HOH A:838 , HOH A:912	BINDING SITE FOR RESIDUE GOL A 702
07	AC7	SOFTWARE	PHE C:38 , ILE C:61 , TYR C:108 , ASP C:124 , TRP C:126 , ACT C:802 , HOH C:824 , HOH C:858	BINDING SITE FOR RESIDUE GOL C 703
08	AC8	SOFTWARE	TYR B:60 , TYR B:108 , ASP B:124 , TRP B:126 , ACT B:803 , HOH B:835 , HOH B:911	BINDING SITE FOR RESIDUE GOL B 704
09	AC9	SOFTWARE	TYR D:60 , ASP D:124 , TRP D:126 , ACT D:804 , HOH D:863 , HOH D:876	BINDING SITE FOR RESIDUE GOL D 705
10	BC1	SOFTWARE	ARG C:14 , ALA C:18 , GLU C:22	BINDING SITE FOR RESIDUE GOL C 706

(no "SS Bond" information available for 1S5A)

(no "Cis Peptide Bond" information available for 1S5A)

(no "SAP(SNP)/Variant" information available for 1S5A)

(no "PROSITE Motif" information available for 1S5A)

(no "Exon" information available for 1S5A)

Asymmetric/Biological 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:139
 aligned with YESE_BACSU | O31511 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132         
           YESE_BACSU     3 MNEFEKACETLRKFMAYMLEKDMKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFGGSFLQ 141
               SCOP domains d1s5aa_ A: Hypothetical protein YesE                                                                                                        SCOP domains
               CATH domains -1s5aA00 A:4-141  [code=3.10.450.50, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee..........eeehhhhhhhhhhhhhhheeeeee...eeee.....eeeeeeeeeeee.........eeeeeeeee..eeeeeeeeehhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5a A   3 mNEFEKACETLRKFmAYmLEKDmKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFGGSFLQ 141
                            |       12    |  |22  |     32        42        52        62        72        82        92       102       112       122       132         
                            |            17-MSE   |                                                                                                                    
                            3-MSE           20-MSE|                                                                                                                    
                                                 25-MSE

Chain B from PDB  Type:PROTEIN  Length:143
 aligned with YESE_BACSU | O31511 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                               1                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137   
           YESE_BACSU     - ---MLMNEFEKACETLRKFMAYMLEKDMKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFGGSFL 140
               SCOP domains d1s5ab_ B: Hypothetical protein YesE                                                                                                            SCOP domains
               CATH domains 1s5aB00 B:-2-140  [code=3.10.450.50, no name defined]                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........eeehhhhhhhhhhhhhh.eeeeee...eee......eeeeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5a B  -2 SNAmLmNEFEKACETLRKFmAYmLEKDmKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFGGSFL 140
                               | |   7        17  |    |27        37        47        57        67        77        87        97       107       117       127       137   
                               1-MSE          17-MSE   |                                                                                                                   
                                 3-MSE           20-MSE|                                                                                                                   
                                                      25-MSE

Chain C from PDB  Type:PROTEIN  Length:143
 aligned with YESE_BACSU | O31511 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
           YESE_BACSU     - -MLMNEFEKACETLRKFMAYMLEKDMKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFGGSFLQT 142
               SCOP domains d1s5ac_ C: Hypothetical protein YesE                                                                                                            SCOP domains
               CATH domains 1s5aC00 C:0-142  [code=3.10.450.50, no name defined]                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee..........eeehhhhhhhhhhhhhhheeeeee...eeee......eeeeeeeeeee.........eeeeeeeee..eeeeeeeeehhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5a C   0 AmLmNEFEKACETLRKFmAYmLEKDmKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFGGSFLQT 142
                             | |     9       |19|    |  29        39        49        59        69        79        89        99       109       119       129       139   
                             1-MSE          17-MSE   |                                                                                                                     
                               3-MSE           20-MSE|                                                                                                                     
                                                    25-MSE

Chain D from PDB  Type:PROTEIN  Length:139
 aligned with YESE_BACSU | O31511 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:139
                               1                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127         
           YESE_BACSU     - ---MLMNEFEKACETLRKFMAYMLEKDMKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFG 136
               SCOP domains d1s5ad_ D: Hypothetical protein YesE                                                                                                        SCOP domains
               CATH domains 1s5aD00 D:-2-136  [code=3.10.450.50, no name defined]                                                                                       CATH domains
           Pfam domains (1) ---------------SnoaL_2-1s5aD01 D:13-122                                                                                      -------------- Pfam domains (1)
           Pfam domains (2) ---------------SnoaL_2-1s5aD02 D:13-122                                                                                      -------------- Pfam domains (2)
           Pfam domains (3) ---------------SnoaL_2-1s5aD03 D:13-122                                                                                      -------------- Pfam domains (3)
           Pfam domains (4) ---------------SnoaL_2-1s5aD04 D:13-122                                                                                      -------------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee..........eeehhhhhhhhhhhhhh.eeeeee...eeee.....eeeeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5a D  -2 SNAmLmNEFEKACETLRKFmAYmLEKDmKSWTELWDENAVFEFPYAPEGSPKRIEGKAAIYDYIKDYPKQIHLSSFTAPTVYRSADSNTVIAEFQCDGHVIETGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKEAFG 136
                               | |   7        17  |    |27        37        47        57        67        77        87        97       107       117       127         
                               1-MSE          17-MSE   |                                                                                                               
                                 3-MSE           20-MSE|                                                                                                               
                                                      25-MSE

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cystatin-like (403)

Superfamily: NTF2-like (231)

Family: PhzA/PhzB-like (5)

Protein domain: Hypothetical protein YesE (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1s5aa_	A:
1b	d1s5ab_	B:
1c	d1s5ac_	C:
1d	d1s5ad_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.50, no name defined] (113)

Bacillus subtilis. Organism_taxid: 1423. (1)

1a	1s5aA00	A:4-141
1b	1s5aB00	B:-2-140
1c	1s5aC00	C:0-142
1d	1s5aD00	D:-2-136

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NTF2 (66)

Family: SnoaL_2 (6)

Bacillus subtilis (1)

1a	SnoaL_2-1s5aD01	D:13-122
1b	SnoaL_2-1s5aD02	D:13-122
1c	SnoaL_2-1s5aD03	D:13-122
1d	SnoaL_2-1s5aD04	D:13-122

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1S5A)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s5a)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 29)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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